From 4f303df2d55b6a08b6e0b5d4805f39c45acc6dd8 Mon Sep 17 00:00:00 2001
From: NiPreps Bot <nipreps@gmail.com>
Date: Wed, 18 Dec 2024 22:05:19 +0000
Subject: [PATCH] docs(master): Update docs of development line

---
 .../sdcflows-workflows-apply-correction-1.pdf | Bin 9688 -> 9688 bytes
 ...dcflows-workflows-apply-registration-1.pdf | Bin 12344 -> 12344 bytes
 .../api/sdcflows-workflows-fit-fieldmap-1.pdf | Bin 13242 -> 13242 bytes
 .../api/sdcflows-workflows-fit-fieldmap-2.pdf | Bin 8710 -> 8710 bytes
 .../api/sdcflows-workflows-fit-fieldmap-3.pdf | Bin 11609 -> 11609 bytes
 .../api/sdcflows-workflows-fit-pepolar-1.pdf  | Bin 14159 -> 14159 bytes
 .../api/sdcflows-workflows-fit-pepolar-2.pdf  | Bin 15105 -> 15105 bytes
 master/api/sdcflows-workflows-fit-syn-1.pdf   | Bin 15941 -> 15941 bytes
 master/api/sdcflows-workflows-fit-syn-2.pdf   | Bin 17660 -> 17660 bytes
 master/api/sdcflows.config.html               |   2 +-
 master/changes.html                           |  15 +++++++++++++++
 master/index.html                             |   1 +
 master/objects.inv                            | Bin 8849 -> 8864 bytes
 master/searchindex.js                         |   2 +-
 14 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/master/api/sdcflows-workflows-apply-correction-1.pdf b/master/api/sdcflows-workflows-apply-correction-1.pdf
index 7037fca09a42da278b5506794fc743d22db9ad8f..e0ff481dee42e35adbd70a3946abe0325ef9af6f 100644
GIT binary patch
delta 18
ZcmccNeZzZ$vI?t_fr+W<W(}1Mi~vDV1@iy^

delta 18
ZcmccNeZzZ$vI?uAiHVWPW(}1Mi~vDU1@Zs@

diff --git a/master/api/sdcflows-workflows-apply-registration-1.pdf b/master/api/sdcflows-workflows-apply-registration-1.pdf
index fdaa3d4291dd37e8a368d1a5e13befe2c80253d5..da07234e280a89dc041ce3934eb677c018a7cd04 100644
GIT binary patch
delta 18
Zcmdmyup?o^H(gdE0~1rT&A)YRnE*{(2P6Oh

delta 18
Zcmdmyup?o^H(gdk6B8rT&A)YRnE*{&2O|Ig

diff --git a/master/api/sdcflows-workflows-fit-fieldmap-1.pdf b/master/api/sdcflows-workflows-fit-fieldmap-1.pdf
index 5c7f000fdd36dd697eb21361b5a86087587c5715..4eb20c48a5316ddc0aa758fc5a4aca9250d8b49e 100644
GIT binary patch
delta 18
Zcmdm$zAJr0g(0hvfr+X4=2}BrCICic215V<

delta 18
Zcmdm$zAJr0g(0h<iHVWf=2}BrCICib20{P;

diff --git a/master/api/sdcflows-workflows-fit-fieldmap-2.pdf b/master/api/sdcflows-workflows-fit-fieldmap-2.pdf
index 95b6bce77a00177e288d1a92393f0fa398055cfb..fc92480eb716a25f2e06dbce0cc5ebd61d2941fe 100644
GIT binary patch
delta 18
ZcmZp3X>-{SsK9DuU}9>qIZR;#BLFyY1(*N;

delta 18
ZcmZp3X>-{SsK9DyVq#>zIZR;#BLFyX1(yH-

diff --git a/master/api/sdcflows-workflows-fit-fieldmap-3.pdf b/master/api/sdcflows-workflows-fit-fieldmap-3.pdf
index fd54b2c5be1fcdae7ee071799ac15e104003dd3e..26fd36d98cd25eab00801e864980f11269493d29 100644
GIT binary patch
delta 18
ZcmcZ^bu(&%xHhYifr+W*W*Kc;CICVs1)Bf>

delta 18
ZcmcZ^bu(&%xHhYyiHVWLW*Kc;CICVr1)2Z=

diff --git a/master/api/sdcflows-workflows-fit-pepolar-1.pdf b/master/api/sdcflows-workflows-fit-pepolar-1.pdf
index 372149e45ba5085a8c562a5bc12e0e5b0789f28b..c12ee6521297a8a219ad92fa7661dfe302210c35 100644
GIT binary patch
delta 18
ZcmX?~cRp_euPLjMfvJJXW+78sCICYM1*QN1

delta 18
ZcmX?~cRp_euPLjciHWiCW+78sCICYt1*!l5

diff --git a/master/api/sdcflows-workflows-fit-pepolar-2.pdf b/master/api/sdcflows-workflows-fit-pepolar-2.pdf
index 9109f132fc9a43ed150536ee9b8e06534625f58d..06ee513743ca6a6a4e0514172f602fc8d87adcaa 100644
GIT binary patch
delta 18
ZcmZoHYb@Ka--6Z1z|_EW^AQVMCICgN2893s

delta 18
ZcmZoHYb@Ka--6Z9#KhQS^AQVMCICgu28jRw

diff --git a/master/api/sdcflows-workflows-fit-syn-1.pdf b/master/api/sdcflows-workflows-fit-syn-1.pdf
index 0db1f0137cdb39eac25a89fb0c2625c55045e019..fab918b677f6b1acdc47105a913ffe2e10248fe9 100644
GIT binary patch
delta 18
ZcmX?FbF^jyvkj|}fvJJ{W)2%$CICY}1*-r6

delta 18
ZcmX?FbF^jyvkj}EiHWi4W)2%$CICZP1+D-9

diff --git a/master/api/sdcflows-workflows-fit-syn-2.pdf b/master/api/sdcflows-workflows-fit-syn-2.pdf
index 6f196efe3ef062bc2ea9d129a4ae56457e989995..920576cdc51f3c43a9e44882c2f82329920e23a1 100644
GIT binary patch
delta 20
bcmey<$@r&}al<YrRwDyb1B=c3ootx^U1kTc

delta 20
bcmey<$@r&}al<YrRznjLWAn}Xootx^U55v>

diff --git a/master/api/sdcflows.config.html b/master/api/sdcflows.config.html
index 38d764fbe3..f428dcc255 100644
--- a/master/api/sdcflows.config.html
+++ b/master/api/sdcflows.config.html
@@ -646,7 +646,7 @@ <h2>Other responsibilities<a class="headerlink" href="#other-responsibilities" t
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="sdcflows.config.execution.run_uuid">
-<span class="sig-name descname"><span class="pre">run_uuid</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'20241218-214420_48899722-e3b6-485e-9f73-2ef64a92cec8'</span></em><a class="headerlink" href="#sdcflows.config.execution.run_uuid" title="Link to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">run_uuid</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'20241218-220451_2d45fdda-eafd-4c2d-baf1-7ba673c29221'</span></em><a class="headerlink" href="#sdcflows.config.execution.run_uuid" title="Link to this definition">¶</a></dt>
 <dd><p>Unique identifier of this particular run.</p>
 </dd></dl>
 
diff --git a/master/changes.html b/master/changes.html
index 7e151cc046..17618a3d12 100644
--- a/master/changes.html
+++ b/master/changes.html
@@ -313,6 +313,20 @@
         <article role="main" id="furo-main-content">
           <section id="what-s-new">
 <h1>What’s new?<a class="headerlink" href="#what-s-new" title="Link to this heading">¶</a></h1>
+<section id="december-18-2024">
+<h2>2.11.0 (December 18, 2024)<a class="headerlink" href="#december-18-2024" title="Link to this heading">¶</a></h2>
+<p>Feature release in the 2.11.x series.</p>
+<p>This release supports numpy 2 and Python 3.13.</p>
+<ul class="simple">
+<li><p>FIX: Normalize BIDS-URIs to subject-relative (#458)</p></li>
+<li><p>FIX: Only fit high-frequency spline for SyN-SDC (#457)</p></li>
+<li><p>ENH: Allow Jacobian correction to be toggled on/off (#462)</p></li>
+<li><p>ENH: Dilate fmap and bold masks during coregistration (#463)</p></li>
+<li><p>TEST: Clear registry consistently to avoid order dependency (#464)</p></li>
+<li><p>DOC: Plot correct workflow in init_syn_preprocessing_wf docstring (#460)</p></li>
+<li><p>CI: Drop CircleCI, using GHA only (#459)</p></li>
+</ul>
+</section>
 <section id="july-04-2024">
 <h2>2.10.0 (July 04, 2024)<a class="headerlink" href="#july-04-2024" title="Link to this heading">¶</a></h2>
 <p>Feature release in the 2.10.x series.</p>
@@ -1062,6 +1076,7 @@ <h3>0.1.0 (July 22, 2019)<a class="headerlink" href="#july-22-2019" title="Link
           <div class="toc-tree">
             <ul>
 <li><a class="reference internal" href="#">What’s new?</a><ul>
+<li><a class="reference internal" href="#december-18-2024">2.11.0 (December 18, 2024)</a></li>
 <li><a class="reference internal" href="#july-04-2024">2.10.0 (July 04, 2024)</a><ul>
 <li><a class="reference internal" href="#changes">CHANGES</a></li>
 </ul>
diff --git a/master/index.html b/master/index.html
index 3575974603..4b6d3c5df4 100644
--- a/master/index.html
+++ b/master/index.html
@@ -446,6 +446,7 @@ <h1>Contents<a class="headerlink" href="#contents" title="Link to this heading">
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="changes.html">What’s new?</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="changes.html#december-18-2024">2.11.0 (December 18, 2024)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="changes.html#july-04-2024">2.10.0 (July 04, 2024)</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="changes.html#changes">CHANGES</a></li>
 </ul>
diff --git a/master/objects.inv b/master/objects.inv
index c49006522b88e2e51cc3eb3e5a202741f10c566f..66483d61b77a649a759f871bec18d532eb03fd68 100644
GIT binary patch
delta 7702
zcmV+x9_itcMW98HiVY>T)G%yFDyc1_HC>~zmtg}CySB^m>ZEEu>()FoN(I+@lL!Pf
z0sE6Z1UCecJN>SccmzOyZ}Ku}9&YkNKar^|0Zfoz@4k_n+mB}Bw=ytuTNinWU`5Zc
zu!85<*L7VyysgmT(9&)Pl0LR$GVtb({)_E2)wkg6pMSmm?Uu^_gvcgW^U{K|i6$vq
za!-kx$x~va4Q_@18y}loyV$nnM|BQrI~WIQHw5=H>OSH1bam-}KIdlyDT<z5M|)Q_
z-R-+KMP9c-ILY1?<U0X^oTtFIWD)UZgF8B`84T=Z+D~*g(d;?xd2e#uOz@xN1q9Z`
zcVd1GXyx{lwCH0}?;3t{EhKN29}bTp`tGu)a{)CHNOgm1+>8s<!RFrq4r+iSxG0ZL
z;u1vv+?>iz|AfGQ=m156v@_(}s{D$Y?(azhs>u<(p7#coRo<cx=j4b26Ic5p|Kk#t
z^*vtZbf^r<d7ET+MV`W1GMu$)@#f|$x}i6c@r?8qUnm0``Sd7-ES3bcQM@j*kE3l*
zFe7*#Ad7>a`MmAQ+lf_%y4Up(b$1&eZ#Hy*_&lbSYMZft0_oNXSvRV8(T=PsU5IKo
zdydQp-Lo=BPCWY7D0>XGT@`2JdD~YyA&bca4L*UYR+lg~!V+_d{%mB$8;j-dJ<5-#
zuJvcVl=pawiR+|Eih?~Y@gpSnDfQcO9gkr`HO!(cd7o<+v?CCRX}A^rX><=mIz}w0
z;hglg#uuc287h3pNB1)E_OiwciwAf5eJ)<f@hk*Jv`(@tgx8#n-fr^a!#k#PQs%}s
zBygr?)Z_4vSll2|^$r=ej+3;TuIU0$p7S;}xlAx7cPZx3R3$*vz^5W2{*6Bl@a4lz
z)>l_e_CcT)G9XQbHbN$ses`!BIcL|?W~k_rxI>|TdFvD1cbcY57wVR8Jmb3Gd3w`#
zsK9FlK8ow=t_PZ`ZUDBZ%;L1UocCs_GkODWcd6rZeoWdR#8qXUWGTq#It9^Nv~*z8
zPy7pFC1WP`IdOtZ^m|pE+c3naY%dLpYra{F(_xe5Pu}o-RE$@<c@v7WP0n?J$T~7e
zIo#ua)z`7meRVj+nVLY4qfg<I60bYXIeAwOiB$+d^3<5oN+9a5`FC|G;6%0SB+;-`
z?I8dbyq~KIybeFdbZv|m<48Yw&d3$4by0QV!CU{d$c0k8d!TW*hp62hAW50#MUm*n
zU<ufYnZETI(~$}FPqO0sgRTgaHdV&@y}ikQ1p)-gr@*vo_&p>z`H;uO4l6Cb7X%lQ
z)Uej#yfMOj8|Q+1H_1i)qjybqWD#!X;?lmtF!|~Z;ugU{9HBTWo!&~Q8$@361*;#-
zDEP(A9)nyAgQz7iXbA|c4KFJR0RWf6)Re}?Vf5q#qF>;lKJ@sZMs0kUngiQ8CrA8$
z&m}|uAI8{T;BhR~sIH2nfz}R(Ln}wXsT)_>->gQ$g*~XDuBtDOW2Sv5p(TZ(&{85$
z)(am>F&vSP?#iQ;6TL;KDU5j(19%acp5hZ8-K%4hoWmJlA9I4%OB@QR0s*~2P5w0@
z8<_Sc>5{v={Gz-ar!Zu&Fbq-IU<+J-1#XtuLst(gf5E_Y({@qYWk0cxK-md16cYWC
z<K-Y;bH2X)5dA=AcDzkt3z3G^e*gICSx@z}V3}6<@6{;JisxAkUz|yeTI9EtCpl$C
z=DXrBnrL|-4r_ZFZqYiIS%F411P*Ex$MHb5sIp5hOLXuvbj)QwI&3GB9si?$^mMQw
zEjXSXY+Os?sLOB+5nP*zNSiFtXs(t;eMEJVeo2l<&L%58fCYIrxYhQuXACXG*a&^s
z|CBKI9}k&}X>t@(BtIxh*;2-Kq|L9Vun=J&@=ypmy2?f=j1T~tE9YPE>1%KJ;47LR
zpCvDkp7kmFd0~6rRm(Q`EzFpID)Za%<w#ssYaky_<CP`Qs6hY1{#Da1S`RA`m=#rK
z%i^uN6KYlsYHM5q`93e$cM&iRip;-~%hCL@T7&#VG?)ZMUfET+fbofHZZake>NF=w
zqXXK!#f`ZjC^x~f^WXfXOIhvk9`2BDl>_-esQ@51wf!S&f3*V@0OY2Bc6L~vzvek1
z80w~faVnp`2TMu|u(ucd2*99j2u>Tcn<LT_2mO7K(^_V5^k{s{VE|7ibU>h+@^Hlu
zDRKKk?vH776gcEpr8tNgpZMshYeEG8xu{(pC+RC%!U)IuyFgE_4C@1<v;ez%F+V0V
zj3WzHJG{F)!I~4G6?rs&9&zMn5Uo8K2<D=hoGI!nm2&7(U4*eCN`0kq7Ja&tJbvn_
zw?M&TLb!;eM~?X_WF*>T7j682R$q03#sF|q$WMLsmMC~k2v?EpfT<8NIg=UVB2}DI
z>npV9F(F(;j*h?e)j6gDfLzor&(`%7En$RXom|NF{-OzoF4aYUSbr+8ueyQA2yxLl
zJ#N@n?2HYDbCS(YH1^iZX$$}th09}-eZ@)`;aC?J`V*Obl@CNlh?CCIQP18|$6OE;
zT<~y`w42CLepQNvnEq61M=?WwRSH}TIo;Y#2F<y=1~*O5J9M+nvPv%6SZC*Iy9(gB
z<=3rcnBE33OPRfY7_dmQmn2U5_LJ4K=+o`x;kL$pdI}s4AvYrIMS5)HrWBe)7geg4
z&TOUiJSK#_NcMe<pFqx`OSKmUd6NU6P4fPR8~|6yPk49JB{EAd+iF-I6YnER!Un@x
z%buS^@1=S{27)<h=4YgP%N0B(gtbVIfpEg0PP3M@IFjFgOWu+VhO?GEociyjcSK_V
zSS#eA1ia)44qd9Xut{VBFL_fYGsaqKhz_mq%#Iy-977?1y7}w5Du}gCRd5C`%}P=$
zxPvdVXb_%G%-LW#YuU1Z6JE-tgkUIK|2VRRo8Sq9It?yq93{g|(u6^s2AAZy4py#z
z?bp4k&>en%!WL{WoP+E>I*6y>fyab!5GjI=cxvov3;+j(<47i+DkoF`kXr4fB`0OV
z<S^`S?ecRD8Z|@zx_%#6Bbr5Kk$xW{2p4ap(>wqxii|d<CE-sXhGp3nm*6)0uqke~
zhwREE3oSeVi=z~gTa{uVqz~lcC}qg6PJ_$Q-sDq%>EL07WEX8Ld$f;PbRu1%l_KX>
zG7WX4NwbpU(N^YxleDQbQA2nJ{lGX4;}A(g4oN?^nb0pryCE~wu#Un>k~vleSQ>!J
zgs_#`pTX4WZ&{j^PD4GJ0Jb{CFEj*y@)0YEB?UtH%kD!=g_S?h+MoltGYM)H*rzGC
zb(R2s-tp5%1N$XdEx-YMVKKY{yTVD~*Z_`9f`$e5XUc7zC4_hUkl)ab30fPpt2^W_
zMi2*RtTjWrkH}H*wNP@$lu)FX3!^Y^!F(8Vf}vhs^ik!4`7kg7fnNHD=ykyy7*Rrz
zUM}=;@`8CVFam*I`onesP~-P*_B`HSFx7&84+OJSK8xAsBYI9{LfA?b4GPilhdxTD
zffP-EnNDd0JpDdd88k1_M=O+WRaN#EyI?7$gGeB8Ku`3DJ&m)Ni8zZc9$5u)v;hb5
zaC$iIW4JgABx!{X<K(4$9M@R<N&rUV29HY!@71F~hLJ7^rm-IkmbKlE(^-oHkp|L#
zuS=)L_p(??bkue5#40AJ4cOniNhr*)o=vHNz+fIFECy;=m!|Pm!AO6n=ozoH5sLT#
zfjyJNcC~{C@KJ<xO2@HZ1G_1WFKeAc?JTNu_*g8Wsz$0{vZgVNThk4dgvLsYk<3%8
zDh;o=8y4uc%g@MCGcbBC4Cd}bTQyyOjrKIEZWsr~ae4t5wR9Ry72GoW*sGB;*srO+
zg+X0=qC|Fr%yiy@m5KCb(|&WI(TFW&!$KT`P~I*yBJy!iANqL8Fqn@QlX#7ERkrI7
z-Vf!IE|#-PCLe$6J~DG~Hzh%zEwJ8BokbYyp#Jp1v0*SDFGP4T9$hSy8?$hK*+87y
zkx?*e@FXw`U>zAkaGS>0sRZ3PJ|cAy3Z)L}jsYV2ZGXwlGwV3zwiz`3LYs}Mttj3E
zoSM+o9o)K>#8nvR5be1T$XVKpfYsoV9ztzJ>cH}*cHG<4bsN)nnA#xq8o~go)v0M!
zenm}3qOe#?S0}$^tbeDh5R{*P6B#P2yhZt0{|2$G7dMRd1EU4OeEkqn=R-QtbDA-J
z@()GQb*Ky|{=Hx{A^e2bczsjk;NcS_{Wi(&IHwuoDW3<~WM59@RVjjP2K0uTxDh7a
z3KP~@{CsU5p^JP1bdgVCx`?<lNr$SW%m5Gc9lW6?=y>$H%swuj@Po5|`1yJ%b8=4*
ze%Bo2-fxWcXVne!1#0F*e+SjDgcxwswL^bhKK)MU7nA#t8ERNZ;Ur0NdB346ZwGOb
z>u)x6z5H1tbAj;{%majmlr1QsNN*R|)3dNX2u?86+lxcqg>~UDKFdIl^A?Zyc(wLx
z5eNN(6AbnCqO0P`t-r8;{w&!YGTHh_GLyL6hFjrgccw)8bX$=$v>x}=OXQSDpKdFX
zOvbTzmVA%$<H@su$O&OMTk$+>a-B3uQE0zfHtSw+86mc6$u|z##|LJSf<l!tlf;%j
z``r8#YmA&OZ$>Hd)x^xmVtq0ufD6#mIE#}e>~q7Jf(vn48g-g~ySR0dWq|}TDt)?#
zQ2K3KD5;#xgm97De?<rQ<`1U1|5)zR;?qAZEQosg?(G-!2wn`#R`4)hnZK-Y^=k2P
z4G1pv3e^}~=CCog2g`<8k*FKY#?}<0WKUxy#z^L=Rh5Q+#D;g5WopfI27tR_(!{%_
z3naK_)2B=2p7S<;1vNVglr=e$psPY*LD4#BcCc|RiK8yr^+QvY7G<L2P^H+5BJ~Ie
zP6yF8r7{5Ql@>|sTY8K_kswvX-)w-6qa(PiSr5s&Ml`jlXq_V}OHlyA0IJog$;I@V
zh+H;+(S-05o}r>k;tmB=K2RDVe%k93d*=wU-+{}YutHFOeolxNbYkNhI<}51n4w6i
zLy(a|GCU|=UQj>PH$BSNJinhkw1?RTy*Dv_JOX%Sg26jfpfe&%T1eRqXxSj!r|L$l
zi9yAPI1t$hGShhrRwlNn%;L1UocFe(L6l~UpZM-l$LIW*v;ozRH~}EJ{;C3YYlf6I
zOOm3kVPQmn)qW@eT!5a&S)4S1e&j~?FQ~DR2p}^dT;%p|u*3;&x8JMk+<L2)asq)a
zKA^I_G$<BtRmA4EDPVpmc`d*${)l%D;u`4#<-pvS)0r`DqTA$L7l=IQ2-A!tj3Ag)
z{e6>^$ATQW1{k_}ux#`aiMlajY)vuv^fXptjAWjFT2*QEG>oK7y6T*hQ{MYKfvu%}
z7X#K=JpFte=b#=b-T0b+H?&@Ym^N8_MX{FUY>Ng(a+od1v%#%`*3Z2$$m*GZA$yJi
zw<syyTe=f^nfJym$keco!by_ka*D^t`=mL?^f6?eH2N=WX9B^5Fr2OUx~MvF1f%Jo
z3A1v42^#=3(<~0bYu8Dc=0%YhH)*mQ(`F|@$ZK0+e9?|%g!Teqw85Ov0!Rpycy=U5
ze1CB9%FT{LCbi$>-80-l8vc$gyaCNKD%;TvXsii|B3<>*>7B(}8F?f>Avjva{M{00
zvy=MkV$3>=!T<5_X4&>8S@o@NGSY(TWv<JA*f@YwgV6~~Lyzb&3`uL7zWli(4@#{X
z<kER(n{N3`MPk(+wM|g5{*+iWH2_ORW;%bxpw+Wf9AqUuWZWk$0#^zJtLlU#n!1Is
zrYS*6V<pB&=BZVcMw>o;@soTV+f*sErw+>Ps4c)suMT-<SLb~ORlN&<sXWJ)HC5Js
z(^-oHkp|MQOQ-cA0MIru^~8?e0<85;eCuu1Hu_Au_R*jI04U?J3PY6w4wcY|1(OH%
z$%GmDvqjsPdS++B0vy=Ob8^K0Tr%{?u1@XP<_PRGdqd!nJsugcf@^)PQC;CJvDNq>
z^5}*Kj)C-~kpx5k6{Idgq0~X$F+ga4JzZsg*lbc4e!*<~O|v)Ez=L{9PY!%kKL-mI
zV6Bff{X)|pjN1fmOW#VZl$faebXsm^dQo;;8IrAiD6MLN;B_MtPKR`3Zq_ht5Hed~
z5XvCZHOXud`A~}e1!~*8Jlgcl-WxY74w-`aj4_Yqso(}feZ4v-U3!X7dD~S&$0j)k
z^=iQlhAO?PE?s>wp8U1Mt9mp~H+74VSxxs7WVXT}ltH9xk~7rgUlZ~YOH0m_z<uV6
zy&szNn}PoZ^WT%#7C(P?!|x}5Nl!_6lpU-m5@;p;{gib7*hVF~|JO;Dr%B!9#cH!%
z?KZoOnqY?8u6OHg^uud%G1_eZDI!;&Nts`g96K{J$L-de_4cZ#eo3i!QtIt<m}r69
zV(J%ydHY-=diw&%{9-7MUC;bN!@S#&99KqWf!nRG2j<;|GGBkmnXiG&*8_83&bw<l
z^W}JHyVdsESR7N}c6~)v)2q?;T3#S557V<XlM5heA<uhqu6(N?e`RcaQy^~Ev|)4d
zSJLLke`{C;;_bh^{_D^0?xxu@l%n$<HLDHrX!}aTvw)H|jP>2{>(Pd~zkT&gWx`kh
z3n*^N>&@7Nybyo-eA^w^gn;hY@X?#t?hGcbOl@QVrQ^uhjqR1Rp$r*cf-6HnNo8D(
zO}x}s2F<7Kq6_G5{o|xEn2AM4o#nfRo46)Tek-$aJ+pB@`{t4~4}c+k0j0HpM}+r0
zK{c@V8O=k^0=i}6LT^Gb?9B3A!%bY%aZO@ESyJX1Y5{-UvfekCc&_*23T)v@7}!n>
zTuJ%!OxN2;Dk<)rx$*y=l&mEfr>8k`$0pT(XP5a%w`lny*LGv7%{g+nen|>K@NYNL
zx)ix~#!+sLq-}mX7}&`NxoNg*umR@4l3(e-bJG|)M-m4{1+;rE9YFhBKbl(N97$Tx
z^@#sRX-j|n{ZfcFp)H&-3=e5cI=(0x&b5^HM`NoT!$|+X7PLRg+atl#8q&@s6WE4z
zNlMFVaoLS1{t8BWHPCJa?UjPIM0`=NFN6_nw|>slmPjo9ucWjuVYDv?+O42{sitKU
z{I!Wzz;^3by;{Bmn74#;(xfLqDNJ!Y+!iqLM{<8rRSrCdvFA;3JGRE-%<^8xa%?v+
z&D+s#qSw6LXf*GD%;SAZuX(3p#)I$HTowar$L5%i2_BxeigFOMvypSOeYoPB*J{p}
zAkLQq=QZbispMqi_Qt>|P-LvxGEP3SZ)BV=Ow-aBwPOPf<$NKXjR^W0B6GCU<Bam<
zR#|_29d9pmEouQJLjtb;zw+y1Cvv4SVeSqK=x+Uj=<iJ^I>nIhg{fUEprmoU8k=|_
zZ6SR=^W?FBl9B#;WI{2C4EdhJO*|j=I^%+3tAT}yD($Mie6<$lNa6#o>|fbsUJ+{k
z=V1Ql1OL^C|GAl8ThDVOspgk+{zWa<4W1F2@KXHSszC)>o+L3bApzf#laU$}e;>OO
z*CY9mJLJ3Cz-<UDG4kWs$koPR#W)--prnAV#x~?b)BP#wR_&@p_ZspMNO=$S+p0xP
zuC2-*!YYsbfmsSkoIi4r-n6~zk}^w*3NKyK>U_q3L^LMprKLBrdFJ6M0l82o4JKd3
z{NKE6yXHcUlue3NRg;&*Te&rRf0_@YixIyFQ&lEsl&zBHc#)jH3lcPE_$&E4dM*Bj
z$>5qv?@BsM*Hx>1p1H_TG5yMmieHbqDthzb=FUzYCc{lBE6}P&4LRF1DO2PjQqCu&
zVu>s@8l}PnvrqA>61Nebx|P!0_7|nK-1n3f?<p(NQ&zO6s3d6f82TRie?~unmppdq
zQ)m}{$N!q<cq;zTWF0UAM_y*=+tMVv%!Z7cx9>^0j<8SDs_d3kF=QG5Z~2dLZc$Up
z+&y4y8y9X-D86}`q*B!%Mpu@(aY=NjA<ZE}HNu9=bTQa2I2D=R@vG6z=&Hoz;{Mmt
z0D(+}pHX+JGD({d3Dnt-f9#KlG^w0aEFD1?3{P3ClGT2*BFCQR<q=OIe_XKQx$k3k
zZ7vpPBzm)ncv{q_%}uu{Ug$L>yLdCT#go7)p~KpWzNLUVtqd5$&47z~94_oAp#x>a
zaZ`ExgMD0LD{>+QbwsH|0)E$Diuk1&|F^ox(;UzHHA?eCp0e!se|dLW@x$cvjD#q`
zKO3ECE1q{89Zk>?K}Y<&_zyjLDp-`<YV7O@Rn5bS3~L;!Q3@pJV>=G8pCX2%&6(pA
z;_wjGu4q8*Bt0RJoOzb_<Ai8P&{^C+tj6ESk?Aj4b=ws?VjWM`lAu@`H9)$l()~j;
z`CbuEvPtxL$Q0!)e>B$E3o<sSS`Uflf=90m&(9j+P=*g@b<6v}aqp{Ho8!M}`<M=6
z8bz8+&|$H{?X6i|%Jx!|_gKg(5YnWy*?uL7(GR24XUfLK-$Pz?C_R<rC?%a$3HbKi
z?XSPQ{uB+DX8h!AzZH4^A2noXCPVqq-E_9}8E<FFWEvQff2SH6#6ddWMxamq&nXZ4
zMw-k4xPY<kwqr%VjOR3A)@J)nB$9zA>JuXtjj60Uw6Cf!EqRe9T8#&%`t;D|X}iwr
zhjMm8-H;2fVg9_^tnh!IX-@nD=f(dQx!Ee~(x!NGneX!=?;gk`Mnur%Go8B1OV^%I
zQNZ;)CGvkFf3qVw*}zNP)0+tu{R?ZNe_05kXFRbwz&l`?o6QAH?kDd~LHzO4he)JF
zB#lX?(r}uM^hx!I21NHhbOj=+$J39gl^dm%M`$giU+m-m=<p)<KR5ryR#>aNU15S%
zvTv*6(xKvE#p8?l`H9n3Z{W5tJR0C^Q5WScF&ho=e~7~^eMWfn!mHc-Ku3m}3=aHI
z2BN4zcqQ55f#Qch?{+0R(ziKRdlJzeUwGzU3{&&B@9fNzl3@%{exRe*?YpRFAY~*N
zq96W2<d10ne|Y9pQ0=NBQn5CMz`LRPgvts}tyLMSIP^var`xC^USl@}E*fx_?zIT-
zS#c{Ye~%5y$T50M0~+;pys1yWbV**UR;wia<C3%c2P?b;%MgaoBZ;{bKo}XMh!|5e
zFtNhwCpgkT1QRZt5mPiUJ;5?@`)R9kx7l22CfGkkt0zg##__C5`MalVZu=$2!!9oP
z*S8;{AIL!lVmXMHL-b36K9b<GCzBUe(_&6Ie@UCYEKJbimD~mNEapHJ7Xd5@Sw8+w
z{vr>%yQHOM5D78QtD+X~>T1aaNJ8J|ml~+bLw;0K)8siR%Oj)f*IqI*k~pKHcxg=y
z`*jsvkC<@|Ib{lGvASi%HgUpL8R_bx53^yg(u37;vIjoBQ)?dM3uKl-HAXp?!6d44
ze~39$=W0`g!(gUA;@x29usoq)&SJ1M1fPf48-=P@S{*SOY!BxS8qC@RR+q;;Q(6JX
zUR@rcspK>t4zG$cWS|5_QPaeWF&MB4A*6`hVK4y-7o&{>U@%}EzC(8~xxtp@A@-`H
zgiTgp=aFj;c{LcYIyHEHex;IIf2OPae;7<H8R+m+`L{nxUiddyrgItrCLE5^)E$fk
zv1oDL81O_uuvL!}AHiqAfyH<p0jN3h3LpV|z?k}5Wq=jv@e78dnt+z94$lG{0s}Pb
zbS{(mcnzR+hf`nlpPvKmTAb&g{~Q)z&+=<?zHp|`K^o$@;aJOAC|a_E78D&Sf7`0D
z%RByrjQh3tUh{wd`+xY`MzgIo@CBi?`nG-b>PN$U0MvG9pOm}J_Js*KerbVAQM~Pd
zH=nDmmTq=aG*jLbJ))AnY%paLSH=4S_~(<;g*>a;Uz#I!=Gx%Q>C$!dKFQ7i9E@|9
zWp7)I-wv2!wXZt-j><0>0=i%Ge>?jAJ!vvrqt6XU+yuT%Dv4fT=Kr~@qAthVoPT*T
zek#m?(DxK@AClBb{jd@VoPl;VUOSWfYtbtDytuzNR`O_1WJV$l>Te&g|K-#Pa_$Ga
zV;k=`nrgtfRsSZ2_Pq<jD8_yIs8~-rfhwPd6H@7cTMIscl0229BxKh?e4ZJaXnLIC
zG2<{MR%cy!^3h$b{sp5I&BMo-=#b<8kz;01+do6D4t<xzMcj3`sN40E7SXQ~CdSw`
z-ga2}Eg3W0?vkCV;*4;Q+!*><*Pwil8o<bTDO=Rwp8HDUvEr@|&3}()25iPOlz&h1
Qu0>z5bkpeff45MJI*zdNNdN!<

delta 7703
zcmV+y9_ZnqMUh32iVan2sbScVR8m_;Yr00Umtg}C+qTQ`>ZEEu>()FoN(I+DlL!Pf
z0lSku1UCeMJN>qkcmzOyuk$i#9&YnOKar^|0ZfozZ@-b7+mB}Bw=ytuTNinWU`5Zc
zu!85<S9M)Hys6OP(9&)Pl0LR$GVuBn{TJJ5s&B#BKmU67+Z~nv5s^)<=A{K^6HQXK
z<em~Wlc&T;8{7*2H$FDGcCl^CkLn!Mb}$aqZV2vY)P2P3>FUydea_DaQWQPAj`ma4
zba!uG7kS+V;Us%oknaQta-IU;kVVAn4esc$W-zduX+P50M6>6#=e^BwGr@n77Z6w%
z---D(pq0B*(xMMZy=(Z*wUE47emFda=uekDoeQXuK&l&5<7Ql-4mSS|a8Lsr!9{s|
z6qg|S=jK#)`X>Z`Mh7Soq@5w(ROMIHbbn78P)&~L^}M&JtnwDUKPN{Nn7G;(`5%|C
ztnctLr$c2>&buW0ROBhFCBs>(7H@98qFZ_+8P7;>@P#t4k&lm3$YM!A8^x<K`!L$}
z1T%u?0kSywna|s<yq#EOsC!)xQFpfi@_IuDh|gnMskRw^E0AuTkaeSa7wyQJ(uJsY
zv**Zs&^;@2<iw+Ijk3p3+f{Kkp0|Ca6S9~*(BKoOYIO-?BP=nO=+8!0ys=pR-lP0@
z>RNx+OL>o{n7B@wq$t?a5<fz6pHjaq*YOx8RKqOFlJ~iGK|2D0n1)-?A4m5vq+`T_
z8qP^?YkWa}nxVpnd~`1pZ!c@Suy}B%-{<0$9M3{vMC&BWLU_&D=<OyyKD=W(CuMGI
zLjq@NMm-Myh{X*eRqv2d>o`ff>6$J8<vDLtlgk8Sa+hKbO;rL!4SXsh;@|k=0AD`b
zWPNqjWFG`-Ap_D>Xd`5D>34^Ek#lxEZH9_2i8~a3nzugDeWz*4bfIqf#xt(_ou@Z_
zhYGw_;G?*%?s}l9>IPto$}CQs%Xx2>I-@u6c9%Ln=f|WCLR?kmNtS|)u2T@bMN0=Z
z{lvc@Rx)N{pA#pzM88+nxeY^%%J$NrxaOO+I2|@={^SkcN5y!xn>V32+vHpqh^!-n
zl*2uLUVR-4-B*WGoT&-)IQkSWDe=1FoRfFukXVHPBu|YQtpuX}ntxZ90!~!BP7)1E
z)gA(1!TY(Y!0YgHOxMPEF^=?;=ZsvzS{GF(9=!EWi(Dwhy9XL~dx+ZI0g{wyUKELL
z43>bcnCV-eF&&vu|0FBEKj?};X;Wpa-`ksiTp&P@d<smfhTlVilMi`Z?6A_}dqHp^
zNeyc)&Ko1lw{b4GcavPyKYG_>M;76BE-vjW43n?!AZ`&H#1V?4(&?>)x<TY6U$FYY
zjDla>>@mp2Fo;?LgO-56+VHZH5CCu~OigKQ97a!0Ao>L!>O+qoYShMusX4Hnb8^Ig
z|6DTk|6z>n1s=yzjq0jM8ffisIJ9yEoVsz9{mp75T-bve>Z<zkIA+?15?WFi3N0l9
zWxepB6vGku=&n3kIni5$n!=bzF@P75=_x+p(Y-o0$vK<>_Aw`Dy~LrADiF|H)Z||i
zvVm!DlP>v`mtT~(;}nJr7KR}z8*G7ptH8|?d+6$6<u4exZrUztyX+_S5hy!hhC-rW
za=aYGYtC19@1q~c%#ODyY$4LH+V3AfJ?p8S7A(^W|GgUJS@Arp;fph=QH%Vx@+7Cs
z$b45EMiVU$#9?hu!!26pGAq!ihQL9M;y50t7FBlXWr+@chK{++M~Cf1vg3b$l%5V2
zqy@*bgN<uR9CaCvA%bf&5owbp8qL+RsE?>l(l5yo$=PJ32e2T|2DjQ?_Kcy07#pEK
z^*<%d{l`P*VwxPq6v+>YQnr+_9clCHDJ(=7h&&X6j;^v%3L^x7=F0gOeEQlOKKP2}
z$7jjQqi21}eqPv~ch#~DehV{yrpo+gd^r-A)f&jh(|BbGG%C=)uz%IGi`K(R1ZG8*
z*|K=6?u43EgW4LGK)%ll_FV)_gCg^<<Z?8>tkxhu5e+6mkymyVE?|73nwyLXgF4Mg
z(&&ITZ*gNT2+B>c?EE)>=~7lZyoWpFTjfALP$~e(O>O_k+F$KJ1pv8!shu5`=dXEA
z2!^`pU!2P4@4=GN0_^PtKLRkQ8-mjY?dFK|#6f>w<g}I<96cHza~Qyr2^|pVraWBn
zLrUDfko#jA9R&{gRVfZ)#wR{{>Y7jiKrU*R$4UB%mN3Gx{w~myE5rK0C@sM5Ud)fl
z4CBax)ei6OPO#<#Xhj}>jYk~$8ANMO27<Y0CTEKJN~IjSR2O0Fh*Do^oJF7RB#)nZ
z>Mc<4m=G=^>5*f;3K@wu*+m;apw(BMpfLcP6!KGFy(J1B6T(#_J76k=OwMG+xJVV}
z)cOkTc}xfwk)z{peRYnh03a8&%d>TTMN1grSSJ^<y}xL}p-Xjt5!Rmy?5l1dGD2K*
zPLCV*6+2^t;hbc%6OFy~avB4`Md9+8WM8ooMmW~Rh5kflU*!Xl5#pqCbkwuA)G-$X
z1s6P=B<&`0lwXx%A*Mf-+EL7qUzGwELr%ALlR<MXufa{z^A6o?v#gSfHrCm>+O7h4
zZuxa<8K$=Z%u;55F9s~q>?MhlzWrqNEc$eNdAO~ypPmATL&%K?dyyU+xhaJv(M6T&
zr88S;J&y@tFOq#9<0p`F=u+*4LEhv5Xp_9ZAqT(}@)O?ObcxK;%eESp$He=HlCZ&W
z*0Sd((R-<0kbz)Mn)w;&-f{(x31KbLV<4O`sMD+^Eso@W_ma0{gW;@Y52yZn=^fD+
z0M-h5C;=~df<u>TEo>5*z)Rkg$&9g<8lpq%JF{a)9>-7!pl<$pt_otUQx%-SOS6*H
z3hv;`EE<HT6LU5g&RVuC;DncQDIpjN*FTPI;U;*(piYBJ8b`@+lQdyar@<w8u7j29
zU;A~hDs+c`pRffR4Cf%bj}GD~c;GQ197KwsBc2+28Uw&V;W(0sr^*Qx0HjuXX~{{M
zFgXnSTf6+6gGSBJzpmd0)`(`2S)|{G2*Sl1=`;_(iXx+pX-W7Kh+$c_#U;4SK5UAc
z?IF7|$wCVcz~U%H<W{9v2<Zd4I7%7vtJC0ev^V*GR62NAA=yP6%O34x7M)0!Xr;)x
zl}tk&Y0|9Zc(j#y;3RG8Ow<sbK|e4~!#G5ekVDeXZ6@@K(Qe2LHLRm>l4OpR0hR`!
zG9hfG_Gd74`dgM}rPEMPCV;I@@e2*XpM1nhVo8Be{<8ZJQ(@%~v^MAf?o5JO1@>vm
zZJi~5fOq`#(ZGHQRts<dUsw#Uz^-soI5vPIlb~UN{h4xGX9?jQKjb&GV}jNO?dlG>
zixI>D8f(pv?jv#(d@YpRF(nk~<-#b;TQDESoM5Pz7kyN@U_K0tK%kfYA$naf2S$`o
zq?ZeQoV;Kj42(dam;SI_0Mz)sn>~;B7fiK(-~+*ImCs`K`G}rVnGm*8MT0^#{GpH1
zX&^-tV5U<V0Z+eARtC+B^wA2XTUC|)#V%M%=^zqF9MBUzVo&2NW+Kj_i$_+09BsgX
zJe(em`xq|H0!dn-!#H^<AICKozY>7axWVHR!h7{7kYS_?f@$mrgJo^E<8;>IK%{|x
z^y|{;@x3fo5*>9NJh6%iY6JH7ZW0PJtY=edATXFm35$Um)}?8DRWQ=uDSE~$ZG<8|
zKw!@#v0d%p0elo8ozija*T8N{<I7s-P&<q296lC{sH%}Fn5=0G<JNRTC84nrV<hv`
zs!GEv?uG@r?ea6S)C`QC3xm1)&{j=<SED_RsvE|EahzTNMlGF2Qw6uoKK5#)4EAfP
zZ(&f^o+y!>ATyn}U}Yk`*|gtWXf$F=*{~4DAe6TYjfi|4)Q3KvG7RS9#Ux%MU6t+n
zgZD%Eq>JV3lF7&4x{u5p+)YW)XA7*iQ)dyzI;cN=aBLXN#|sf&j7Jv><;E<3Ts9D=
zc4QQc8axTi0$4|e5ZtEmbt*wOj*m!PghHu<x?_Nde%oJi^UOL<xorlGztCo*YAcF2
z0jDN3bqBYuC2<u7Iz)Re1ag-4B49PRq=!&jkvg!vsU7z=b=}7F9i}!&y@oJ=YISN_
zm0wZQkti(I($&dt80+6DD+J|#=R}6eDsNGK*1th)>%}djea~n?Fke4J)cKH3^qgjl
zpZr6SbR8-Kihm~<O$a~XHD2EoIe7R4Nxw_7Pn^??@s!VlY_cz>@~RZUHUoOYP236-
zZ-fc!EPlQ=kI+Rv0=me@FkM94nWRHiQf7b$`VQVu6LdU!Rc0R+Px!%qS^RvxlsUO4
z2)}C%a_=|B`m^eW`2sa_qQ8S`SV9cA>Dr;cE}woU^oz-T$P6{Cqi~WWxxC-dmA8X9
z$@SM8x?cXQk-5P53g!VqL&_GEP^7mD?CDup9|R{D>g~lL@4~up7@uXJ$9ap#d%Rlv
zwTOd$!3l<Xd(l<#<knw*Sbvu64w-CyB$-KEZo{o`vpZ8FeY&kk8d{Hg>LqeYq))dM
zNhaf1JWIYu`SIl0K;(oloUM2sHn~okq$spsEt_>OxQq~6wd5NI?c)QpNI{`WnMq<x
zpM7qAiZw<~mp7vn`D$WjWU)RO6Tk)NX`IDL6ZW~`Ou>aXEsZ*V&0X9&$+AEK8I?ZW
zLn!^WEtFJFW<t2g?Z2V}eDep>+<z?haq;P&78XQ3efRbYdIT>9W-E9YugqW8xO%nt
zxCR85dWC8XE_2uz+k<7ptVq-iW@BrLQL?A85@RIu)T&CuKVrkX%QCfQIs?F6F=^sm
z(*+XTv+2{Na?g2xn}V7h1<INnNzhfHu%KuiG&|V1mc&t)?E0apN{celai~)4MUi?0
z1gC>&n^GA7_DYMS^({R{p-7M_;%_!U$I%g7)~ttQT_c*>RJ6_!m8B>EVF1<Y)Z}7%
zO++pmz-U7F3C~c`C2@xWDjz6~5I^npiM?|K+3&#RPgo&;C_g8}3p%m!4INuY7R*qj
z)FH@7AsHSNFE6N{>YE<rYo6cF9@@j~gWj7MKOO<RGQr>-D$p5`B`u`v2DEID?NfE5
z)x@A;L>!3h1exi)1uGL<RAzD7T+Vx2(I84Q#!q~AspE5gOxl3zN1OnVTz^#oyEQ{f
zn<Yun*03;tqG~^s04_jJ<19{^KtFP$`xn&MNCc3X5H522H(25Xx7+Vkb#A>?OF4l+
z7avgBUK$jOw<==u+Y~TAl)M&T7k|V%2XT$`fpTDO%<0S+H_>f!t_wsSbcAU}5=IbA
zs{X!7%40!}TmuYUJy<q+iA3EPF}9`{e0mxyF-9_fPpzsndKyMjCS7&T$tmysoxs*o
zzl#CuES`Qoj&o3tlx}>@zZ+UFK}?%0zM@#ma<)Z-B00<!<k{d>LF?z<7-aQKz>q!1
zfLoN5?k(L3z07;#7G!EzN8uz%ayiB0<9*VcWBM4fP8$6ewljfXLKx0gd|gzXID*l1
z(1clkxr7Y>nrRk?;I-?dO!J~hjGHuBj%l-#Amp{JFurI<GD3TSFxp^FXaOVyN<2G~
zBfdYlc;#ltA(Pr~^6nY#APs-V7T$p78I|p51~k@$M3Jug=k(6vt&BX9pAa0aV*YLk
zwAo4hbunh0#o+&Vc(ZJKldSsIHyLR`^)lCgWo#V4sln)krJ+ak7>1;^O<(@pkq4z#
z4RYzcvrV^rrXsOwkJ=`vSbs_^ni_zmA~T)8V$kYYDh{%e9y0Ee7J(~;f>m`w5>4Gg
zSksgsrLhuYB=gj&N~2AmzW7PLj%}(G+EWMRcGMPNrB{c%v#awygR0&Iz*L@N%bF^G
z>*=h;fk*@C*QL|?5CCYKn0jJIZvobNC%*NzY8!nfUHj-ye*l#6ScRcV0f$Ox#Dd8K
z`((ll{n?`JOg*zRVF3>8<vBUxe=Zq%WLKwlY;y#5n!O?L$R3Z3Si!Zv)~K%Vme^{1
z5P5XN1IIvm(nx}#{|ZtUp-}3e?ie6{w4ScAKWsLs3%_7C{-)WRYT!XVr6&hIs-J@e
z3$WHln|`6`55{c*x212TR!U4%emX5TGrcIgtqjT5K9p9qK=8Ve38zE4F*j=%HVB!m
zFbHK3>6&D=h<qr;{sOgaULI}wX77!g6^Bg0e8!kZ^Hgwyp}t<7lP*2Qr@ZY$s$-L!
zgL<{#21AuzRhO>57*GCM;#EDGr<=OP$gHOO2{Kz@5XvCZHOU!j@~;VbiKQiHO5i^8
z#oiB1`t87fi}^p3))qg1pN8L0{*s=O@+do4PbAPv`ui#A{;`cpbpNlDEKifV$&1xy
zyV`Ab8#TcUw_Wen+vtZ^<YKhh{!>J*K9e%PAUSqsW{%sfH|y<HPyK>Y@1)e*8<=Q;
z+hXeHf_ZzR5xsp5WPUyr$F667u3_G7NRBHbv%u}v*8}rzLz%CC<jmJV=IepEFX!F0
zocVIRwB2fZZ7hx{aJ#;us_E5edo3>zmWS!tn#l!_w2+&goGafd$X^;;-xP?OHEr0O
z{H3({@!uL&fq3(8um1Y;+fUQ%8A{Q4kDAqnc(i?~;aNaQ8^-!>`SoZ+-QT`^rZQnH
zfCUsc<@IK4LS6`eeZK7uY(hYHZ20I+Y<C6|SEe?yfYNbf?8f#=+E9j!FTj-{prkUc
z#wK3qD}(0KcF_fNxBhWb8O+3@qaM({xg^a4V7OgCX-VPU`i>{42HifRc{o@=x2(_h
zCKN-$EZ;TU#5EmrBqpwvCT`$f+zi9~W^Cd{@5L3^!j&+8u$>sVlJe)7t|yRGQrtUp
z!~8udSxYcZ9dqQ4O?dy#F7r`n(JDo*?Z#A_bL4LQf)s?{-)^LJDRS+MBhVa4+x&Jg
zu#*o!(`?sZ1I&RXztVvl)A%+=5(h>Fw7ZcGZhfvFO)YVbBrWKA#Q&qTCH{UXM4QkS
z&KQPAekL7%Ula}JTFU#Qu~m*?r2k(F+8^cZk>F_!X~+2qY{R-FrDe6a>_!xS1*5$h
zXt#p)N<mv9zTnmu!U(oo-!Qc$63g-{DeVgw?TdkSD`;P+Y1!m^ZK4&h-TGy(mQT;~
zmT*p*^aLn{DQ<_`0w(@IE~?6b=P>rXDQ?HsUz}Ng-s@P7?FOcKJ6h@YnztK`<{glE
zyocyD?^Miq@ZFlrVnFTK9P=T;!}C^A4q|pTa*mevSDf=&&G`bv`C{O_=A18-oNV0Q
z7&rxrj5S-v$w&5$jPto^S{kEvY@nf>&!w{wL0>~;j&@<3QNG+NtFPmwzph0spkzqE
z)&Ez2eqHPmu2d$>-C+UUt)CP9y$MC981g+gwTlImG>(^J6VIhBq|axbJQh$g(qE5E
zC?=61-woWv&9Dy{7Zh6!EKF2sSM}wqwJ=8#A8=*=$}aPYQ1jn_`ELgPs}cW=nO|Ga
zb0n$e7jynaE!Pd6n($Km+p0kYTAuPSF(Cne-;qnW&wY!;r73@l>W()*lLHIrj@`TZ
zB(6vDA$Q1kwSn6ZSYqVIv5~8d!HRJ>T0ltwU5#zXho<{e(yiK6iS9MzBarg`=C@Ug
znp|6zJ%m*r`vbESk{EpCBE6ydsY}W%DJr~lNvrc2{}Iu6p_i84WagQNJNV>6oivz#
zd=>M5^Rn%l3pwsJDOOcYUf^!!*6eBCk1j_1B1~18oKdz)n&U-sHZDleoZ+wJ@935I
z8zzHmCcP`^FkM%z_Ic(aN5%9jFDiaL>Z<7V``b@;@-P{0N?CzcHEPJYqe+<}50P>{
zAr(txsnIAECYXIDUzNCx_|&bG=B~egD6Qqbr>uBSS&^QyqCG_=L7T_W_s}=`dAj70
zNS{Kx@LT@ZG{;l%hbHTQ894GXL*JGr*=06l+`f57%5{W&npS1EtcoGi0C>ZHjB|^c
zQs(XfW81iJi$d`|(j=9tem}ah%#BN;Lk(#T8LAOBT&9b`cEPF0^p;<ZZbw&tB_<d5
zzm^6FWGeiOx>J=&+Js1;&VFEjM5IaOq+;m^x?p(9;)tyFn-w{dJTH%U3i;!L70-Pi
zvuks)7$DK>O~lipK5cHgP4PmnA=$-Sqb;5URtX)}R`d-5)M;hF7;Xn#)Z=hrM+qG$
zBaWNO;~&%G5?hheBB&!uB@*y|+x}9-FU|PB)kU7>c;2s3nji9%Wxvn6(~2MTo@XR{
z2>#jVOk451<>+XFjtDy9XSu)c(Nn>q<W^&6PpE1hR%BS?P>oU`K_7Q<fc+FP9Bs}V
zrx1sSuy#d*T_@=Yf#l4yyc;J(LxRrY{$Vx#evM3j$*S9~*zxChvX%sYtkS3f(oL1_
zAEL>(gm{uoqR&I7C}&}-#$J%ILDhOlq!m1RWq5wp2!}GfKdW2bdyaco&DtFQP20zG
z7}F@yWP%Qh6>e|M>Qc6sn!IB|R)LTvrOoy$NsN9Nr9M+OF8+@2szd3iB*z@-tV+Ol
zZ|{En<<-Y%xHRJ@=kBe4$h-NdAwx46%7^Zzv!%~?H%lhdz>qxE&>#-d`8EQ5?0-&q
z*!Rn14!{MBZMPjO`em%839~laZz7QlJW-z*u}Dc})uDY=eQC){F41Z{IMt_zHc#7i
zUO$wx)8mF*cn$OC-DZXV`%H7<A2=`mzsSv2S(i4&o6CHk7kT%8KqfIFf-axw)Ky-(
z_JoQ8uIDL{{}Y)V$*BWg>Ym<CsOVo<6aC9V5Iuj1)dAiC)7)$>XmUS!pA^I&KE97c
zT13*AWGW4(*+`#Mk7z)2??YE0qIx|2m|D42T6u)lLi)u%{*MkXa{qJlUu=c7%G(tt
zSS9<mDlQ!=9#%Ym_LrZZIBoSBZVSVs0nQe6QQi`>(EyJ)+|p-+M=!j(%@1^BsL9~K
z4@@A68iZGpEgmR-`15X8q9c9Naz$g@;|tIHi(zX1?ya49QZkGo$`5q(x_cY-45W+%
zL-fNxi2M=F{}0cc3aVXIL@L(C5O_CKpHNxhskJIY6^Gt`$l!DvRm5xTrocr5&eFXW
z;XNyEh2^n989CyPX+WdCjyLt`moCYR)oPWbe_V2Q|6qleU>U;jd6X}g0th366cJ;J
z1}0Wm{RBrEh+x8nGh&JcrYBe?Za-~R?lzk%%>?_WX!Rti**Kn6DSt1N&27Krc-X}S
z|LX32^aDA6WI!wj@p6d1<=;p7d-i1VGHF`O2`6c@7kLR<ye_+dp2Zxf;v#@0A<M_#
zmtW*zcbBxZ3?d=sc~#WnJz6cf07>Zk{89r|dB~4yYMMMJWqD+D{n|@LMiOUK6fdo*
zVZW}T>k%`~A*W2?ERME}*d~UzDkEK8^dT?|R(i01I)?SYr*~@2<8Oh?GN{HV=Q5Z?
zbq+Cy>RfG#a2U+=$FCdg9G0gC%vlVUhQRO;d$ZW|hEVe++rycF2D3In&*d@6lvcoT
zQJ2SCDml#ux2s|R87P4f&NQ)H3<j*i`zWGn7)*ddxoFSmHyE%Et)V+K++fS{fO*w1
zza}exu(QH72e29pSe@uQKU-4Ctv_#7enh2~40JH5{JR__FZ}x`(;12Y6As5*>JF`f
zShP3`40u`}*s8~AjNo(Hz+ya)=hGZV1&{zf{7d~EF~AD+XavJCN<d3i2U`ISXaSma
zIy1?9^aaqm!-*{VPs4$BEzVldf2s<wXZa<6IA1u^=O7L7+;HUNEKDrfK?{lwm2K77
z<sE<C#r;}*OZmV5{XhI|quJIP_<~ScecQf#`J>@J0BSq5Ps-h9``m;azqG)mDBgC!
zo6pr&OE<eInkjFJ9#KhOHkh)BtK$6u{PW4_LY`IaFU=7<b8T?ubm=;JpJZnM4#v5E
z%d)pE#%~8qvD#N1en;gO3<2G*`5k@#o-`S*(HjF2H-RscN}?B-`F}2}sLSy-=U<+T
zp9*sz^gRXKha`1UKdeLoXP{k;*UserTC|EjFYfP+l|0%LnUP3?`nw10e>ru6oXNrN
z*v9*frW!DA)xU|MeeZ%WigBMlD%O*KPN2%C;e=Fr7}kPMpd?QvDGAwikY|P_njU9(
z%s7mR)maxhd~{c<f5B))^YAeyI^_6&<Omql_Ro;3L*FHF5qBLf>URC4Mf9tLi7|GK
zw;h&#N5;&yyJV-TI3wI6H->)JH7MVs1~777$`&=a=f2c<thnn#^WWo{0h=)r4dvgH
Rylc@{EZsEv{U7RjZFBU_;5`5U

diff --git a/master/searchindex.js b/master/searchindex.js
index 7bdd9ab13e..dfb121f9bb 100644
--- a/master/searchindex.js
+++ b/master/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"0.1.0 (July 22, 2019)": [[38, "july-22-2019"]], "0.1.1 (July 23, 2019)": [[38, "july-23-2019"]], "0.1.2 (October 10, 2019)": [[38, "october-10-2019"]], "0.1.3 (October 15, 2019)": [[38, "october-15-2019"]], "0.1.4 (November 22, 2019)": [[38, "november-22-2019"]], "1.0.0 (November 25, 2019)": [[38, "november-25-2019"]], "1.0.1 (December 04, 2019)": [[38, "december-04-2019"]], "1.0.2 (December 18, 2019)": [[38, "id1"]], "1.0.3 (December 18, 2019)": [[38, "december-18-2019"]], "1.0.4 (January 27, 2020)": [[38, "january-27-2020"]], "1.0.5 (February 14, 2020)": [[38, "february-14-2020"]], "1.0.6 (April 15, 2020)": [[38, "april-15-2020"]], "1.1.0 (February 3, 2020)": [[38, "february-3-2020"]], "1.2.0 (February 15, 2020)": [[38, "february-15-2020"]], "1.2.1 (April 01, 2020)": [[38, "april-01-2020"]], "1.2.2 (April 16, 2020)": [[38, "april-16-2020"]], "1.3.0 (May 4, 2020)": [[38, "may-4-2020"]], "1.3.1 (May 22, 2020)": [[38, "may-22-2020"]], "1.3.2 (August 14, 2020)": [[38, "august-14-2020"]], "1.3.3 (September 4, 2020)": [[38, "september-4-2020"]], "1.3.4 (July 07, 2023)": [[38, "july-07-2023"]], "1.3.5 (February 14, 2024)": [[38, "february-14-2024"]], "1.3.x series": [[38, "x-series"]], "2.0.0 (January 25, 2021)": [[38, "january-25-2021"]], "2.0.1 (March 05, 2021)": [[38, "march-05-2021"]], "2.0.10 (December 13, 2021)": [[38, "december-13-2021"]], "2.0.11 (January 22, 2022)": [[38, "january-22-2022"]], "2.0.12 (February 08, 2022)": [[38, "february-08-2022"]], "2.0.13 (April 08, 2022)": [[38, "april-08-2022"]], "2.0.2 (May 11, 2021)": [[38, "may-11-2021"]], "2.0.3 (May 14, 2021)": [[38, "may-14-2021"]], "2.0.4 (May 18, 2021)": [[38, "may-18-2021"]], "2.0.5 (August 24, 2021)": [[38, "august-24-2021"]], "2.0.6 (September 1, 2021)": [[38, "september-1-2021"]], "2.0.7 (September 30, 2021)": [[38, "september-30-2021"]], "2.0.8 (October 15, 2021)": [[38, "october-15-2021"]], "2.0.9 (November 16, 2021)": [[38, "november-16-2021"]], "2.1.0 (May 26, 2022)": [[38, "may-26-2022"]], "2.1.1 (August 29, 2022)": [[38, "august-29-2022"]], "2.10.0 (July 04, 2024)": [[38, "july-04-2024"]], "2.2.0 (December 09, 2022)": [[38, "december-09-2022"]], "2.2.1 (December 12, 2022)": [[38, "december-12-2022"]], "2.2.2 (January 04, 2023)": [[38, "january-04-2023"]], "2.3.0 (March 01, 2023)": [[38, "march-01-2023"]], "2.4.0 (March 10, 2023)": [[38, "march-10-2023"]], "2.4.1 (March 20, 2023)": [[38, "march-20-2023"]], "2.4.2 (April 20, 2023)": [[38, "april-20-2023"]], "2.4.3 (April 24, 2023)": [[38, "april-24-2023"]], "2.5.0 (June 01, 2023)": [[38, "june-01-2023"]], "2.5.1 (June 08, 2023)": [[38, "june-08-2023"]], "2.5.2 (November 09, 2023)": [[38, "november-09-2023"]], "2.6.0 (November 10, 2023)": [[38, "november-10-2023"]], "2.7.0 (December 18, 2023)": [[38, "december-18-2023"]], "2.8.0 (January 10, 2024)": [[38, "january-10-2024"]], "2.8.1 (January 22, 2024)": [[38, "january-22-2024"]], "2.9.0 (June 13, 2024)": [[38, "june-13-2024"]], "Author list for papers based on SDCFlows 2.0.x series": [[38, null]], "BIDS Specification": [[44, null], [44, null], [44, null], [44, null], [44, null], [44, null]], "CHANGES": [[38, "changes"]], "Configuration sections": [[5, "configuration-sections"]], "Contents": [[41, "contents"]], "Contents:": [[40, null]], "Data: a brain": [[45, "Data:-a-brain"]], "Direct B0 mapping sequences": [[44, "direct-b0-mapping-sequences"]], "Discovering fieldmaps in a BIDS dataset": [[44, "discovering-fieldmaps-in-a-bids-dataset"]], "Estimation tooling": [[44, "estimation-tooling"]], "Examples": [[40, null]], "Explicit specification with B0FieldIdentifier": [[44, "explicit-specification-with-b0fieldidentifier"]], "External Dependencies": [[42, "external-dependencies"]], "Fieldmap estimation: theory and methods": [[44, "fieldmap-estimation-theory-and-methods"]], "Fieldmap-less approaches": [[44, "fieldmap-less-approaches"]], "Fieldmap-less by registration to a T1-weighted image": [[44, "fieldmap-less-by-registration-to-a-t1-weighted-image"]], "Implicit specification with IntendedFor": [[44, "implicit-specification-with-intendedfor"]], "Installation": [[42, null]], "Instrumental options": [[39, "sdcflows.cli.parser-_parser-instrumental-options"]], "Library API (application program interface)": [[0, null]], "Logging": [[5, "logging"]], "Methods and implementation": [[44, null]], "Named Arguments": [[39, "sdcflows.cli.parser-_parser-named-arguments"]], "Options related to BIDS": [[39, "sdcflows.cli.parser-_parser-options-related-to-bids"]], "Options to handle performance": [[39, "sdcflows.cli.parser-_parser-options-to-handle-performance"]], "Other (unsupported) approaches": [[44, "other-unsupported-approaches"]], "Other responsibilities": [[5, "other-responsibilities"]], "PEPOLAR techniques": [[44, "pepolar-techniques"]], "Phase-difference B0 estimation": [[44, "phase-difference-b0-estimation"]], "Positional Arguments": [[39, "sdcflows.cli.parser-_parser-positional-arguments"]], "Pre-1.3.x releases": [[38, "pre-1-3-x-releases"]], "References": [[44, "references"]], "SDCFlows": [[41, null]], "Sampling that brain and MRI": [[45, "Sampling-that-brain-and-MRI"]], "See Also": [[18, null]], "Standalone command line usage": [[39, null]], "Submodules": [[1, "submodules"], [8, "submodules"], [16, "submodules"], [24, "submodules"], [26, "submodules"], [28, "submodules"], [32, "submodules"]], "Subpackages": [[26, "subpackages"]], "Susceptibility Distortions in a nutshell": [[45, null]], "Thanks": [[18, null]], "The B_\\text{0} field is not absolutely uniform": [[45, "The-B_\\text{0}-field-is-not-absolutely-uniform"]], "The effect if the PE direction is reversed (\u201cnegative blips\u201d)": [[45, "The-effect-if-the-PE-direction-is-reversed-(%22negative-blips%22)"]], "The effects of this physical phenomenon": [[45, "The-effects-of-this-physical-phenomenon"]], "The second ingredient of the distortion cocktail - acquisition trade-offs": [[45, "The-second-ingredient-of-the-distortion-cocktail---acquisition-trade-offs"]], "Unwarping the distorted data": [[44, "unwarping-the-distorted-data"]], "Usage": [[5, "usage"]], "What\u2019s new?": [[38, null]], "sdcflows.cli package": [[1, null]], "sdcflows.cli.main module": [[2, null]], "sdcflows.cli.parser module": [[3, null]], "sdcflows.cli.workflow module": [[4, null]], "sdcflows.config module": [[5, null]], "sdcflows.data package": [[6, null]], "sdcflows.fieldmaps module": [[7, null]], "sdcflows.interfaces package": [[8, null]], "sdcflows.interfaces.brainmask module": [[9, null]], "sdcflows.interfaces.bspline module": [[10, null]], "sdcflows.interfaces.epi module": [[11, null]], "sdcflows.interfaces.fmap module": [[12, null]], "sdcflows.interfaces.reportlets module": [[13, null]], "sdcflows.interfaces.utils module": [[14, null]], "sdcflows.transform module": [[15, null]], "sdcflows.utils package": [[16, null]], "sdcflows.utils.bimap module": [[17, null]], "sdcflows.utils.epimanip module": [[18, null]], "sdcflows.utils.misc module": [[19, null]], "sdcflows.utils.phasemanip module": [[20, null]], "sdcflows.utils.telemetry module": [[21, null]], "sdcflows.utils.tools module": [[22, null]], "sdcflows.utils.wrangler module": [[23, null]], "sdcflows.viz package": [[24, null]], "sdcflows.viz.utils module": [[25, null]], "sdcflows.workflows package": [[26, null]], "sdcflows.workflows.ancillary module": [[27, null]], "sdcflows.workflows.apply package": [[28, null]], "sdcflows.workflows.apply.correction module": [[29, null]], "sdcflows.workflows.apply.registration module": [[30, null]], "sdcflows.workflows.base module": [[31, null]], "sdcflows.workflows.fit package": [[32, null]], "sdcflows.workflows.fit.base module": [[33, null]], "sdcflows.workflows.fit.fieldmap module": [[34, null]], "sdcflows.workflows.fit.pepolar module": [[35, null]], "sdcflows.workflows.fit.syn module": [[36, null]], "sdcflows.workflows.outputs module": [[37, null]]}, "docnames": ["api", "api/sdcflows.cli", "api/sdcflows.cli.main", "api/sdcflows.cli.parser", "api/sdcflows.cli.workflow", "api/sdcflows.config", "api/sdcflows.data", "api/sdcflows.fieldmaps", "api/sdcflows.interfaces", "api/sdcflows.interfaces.brainmask", "api/sdcflows.interfaces.bspline", "api/sdcflows.interfaces.epi", "api/sdcflows.interfaces.fmap", "api/sdcflows.interfaces.reportlets", "api/sdcflows.interfaces.utils", "api/sdcflows.transform", "api/sdcflows.utils", "api/sdcflows.utils.bimap", "api/sdcflows.utils.epimanip", "api/sdcflows.utils.misc", "api/sdcflows.utils.phasemanip", "api/sdcflows.utils.telemetry", "api/sdcflows.utils.tools", "api/sdcflows.utils.wrangler", "api/sdcflows.viz", "api/sdcflows.viz.utils", "api/sdcflows.workflows", "api/sdcflows.workflows.ancillary", "api/sdcflows.workflows.apply", "api/sdcflows.workflows.apply.correction", "api/sdcflows.workflows.apply.registration", "api/sdcflows.workflows.base", "api/sdcflows.workflows.fit", "api/sdcflows.workflows.fit.base", "api/sdcflows.workflows.fit.fieldmap", "api/sdcflows.workflows.fit.pepolar", "api/sdcflows.workflows.fit.syn", "api/sdcflows.workflows.outputs", "changes", "cli", "examples", "index", "installation", "links", "methods", "notebooks/SDC - Theory and physics"], "envversion": {"nbsphinx": 4, "sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["api.rst", "api/sdcflows.cli.rst", "api/sdcflows.cli.main.rst", "api/sdcflows.cli.parser.rst", "api/sdcflows.cli.workflow.rst", "api/sdcflows.config.rst", "api/sdcflows.data.rst", "api/sdcflows.fieldmaps.rst", "api/sdcflows.interfaces.rst", "api/sdcflows.interfaces.brainmask.rst", "api/sdcflows.interfaces.bspline.rst", "api/sdcflows.interfaces.epi.rst", "api/sdcflows.interfaces.fmap.rst", "api/sdcflows.interfaces.reportlets.rst", "api/sdcflows.interfaces.utils.rst", "api/sdcflows.transform.rst", "api/sdcflows.utils.rst", "api/sdcflows.utils.bimap.rst", "api/sdcflows.utils.epimanip.rst", "api/sdcflows.utils.misc.rst", "api/sdcflows.utils.phasemanip.rst", "api/sdcflows.utils.telemetry.rst", "api/sdcflows.utils.tools.rst", "api/sdcflows.utils.wrangler.rst", "api/sdcflows.viz.rst", "api/sdcflows.viz.utils.rst", "api/sdcflows.workflows.rst", "api/sdcflows.workflows.ancillary.rst", "api/sdcflows.workflows.apply.rst", "api/sdcflows.workflows.apply.correction.rst", "api/sdcflows.workflows.apply.registration.rst", "api/sdcflows.workflows.base.rst", "api/sdcflows.workflows.fit.rst", "api/sdcflows.workflows.fit.base.rst", "api/sdcflows.workflows.fit.fieldmap.rst", "api/sdcflows.workflows.fit.pepolar.rst", "api/sdcflows.workflows.fit.syn.rst", "api/sdcflows.workflows.outputs.rst", "changes.rst", "cli.rst", "examples.rst", "index.rst", "installation.rst", "links.rst", "methods.rst", "notebooks/SDC - Theory and physics.ipynb"], "indexentries": {"add() (sdcflows.utils.bimap.bidict method)": [[17, "sdcflows.utils.bimap.bidict.add", false]], "analysis_level (sdcflows.config.workflow attribute)": [[5, "sdcflows.config.workflow.analysis_level", false]], "ants_float (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.ants_float", false]], "apply() (sdcflows.transform.b0fieldtransform method)": [[15, "sdcflows.transform.B0FieldTransform.apply", false]], "applycoeffsfield (class in sdcflows.interfaces.bspline)": [[10, "sdcflows.interfaces.bspline.ApplyCoeffsField", false]], "as_path() (sdcflows.data.load method)": [[6, "sdcflows.data.load.as_path", false]], "as_path() (sdcflows.data.loader method)": [[6, "sdcflows.data.Loader.as_path", false]], "au2rads() (in module sdcflows.utils.phasemanip)": [[20, "sdcflows.utils.phasemanip.au2rads", false]], "b0fieldtransform (class in sdcflows.transform)": [[15, "sdcflows.transform.B0FieldTransform", false]], "bidict (class in sdcflows.utils.bimap)": [[17, "sdcflows.utils.bimap.bidict", false]], "bids_database_dir (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.bids_database_dir", false]], "bids_database_wipe (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.bids_database_wipe", false]], "bids_description_hash (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.bids_description_hash", false]], "bids_dir (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.bids_dir", false]], "bids_filters (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.bids_filters", false]], "bids_id (sdcflows.fieldmaps.fieldmapestimation attribute)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.bids_id", false]], "bids_root (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.bids_root", false]], "binarydilation (class in sdcflows.interfaces.brainmask)": [[9, "sdcflows.interfaces.brainmask.BinaryDilation", false]], "brain_masker() (in module sdcflows.utils.tools)": [[22, "sdcflows.utils.tools.brain_masker", false]], "brainextraction (class in sdcflows.interfaces.brainmask)": [[9, "sdcflows.interfaces.brainmask.BrainExtraction", false]], "bspline_grid() (in module sdcflows.interfaces.bspline)": [[10, "sdcflows.interfaces.bspline.bspline_grid", false]], "bsplineapprox (class in sdcflows.interfaces.bspline)": [[10, "sdcflows.interfaces.bspline.BSplineApprox", false]], "build_workflow() (in module sdcflows.cli.workflow)": [[4, "sdcflows.cli.workflow.build_workflow", false]], "cached() (sdcflows.data.load method)": [[6, "sdcflows.data.load.cached", false]], "cached() (sdcflows.data.loader method)": [[6, "sdcflows.data.Loader.cached", false]], "check_path() (sdcflows.fieldmaps.fieldmapfile method)": [[7, "sdcflows.fieldmaps.FieldmapFile.check_path", false]], "checkb0units (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.CheckB0Units", false]], "checkregister (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.CheckRegister", false]], "clear() (sdcflows.utils.bimap.bidict method)": [[17, "sdcflows.utils.bimap.bidict.clear", false]], "clear_registry() (in module sdcflows.fieldmaps)": [[7, "sdcflows.fieldmaps.clear_registry", false]], "cli (sdcflows.config.loggers attribute)": [[5, "sdcflows.config.loggers.cli", false]], "coeffs (sdcflows.transform.b0fieldtransform attribute)": [[15, "sdcflows.transform.B0FieldTransform.coeffs", false]], "convertwarp (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.ConvertWarp", false]], "coolwarm_transparent() (in module sdcflows.viz.utils)": [[25, "sdcflows.viz.utils.coolwarm_transparent", false]], "cpu_count (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.cpu_count", false]], "crashfile_format (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.crashfile_format", false]], "cwd (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.cwd", false]], "debug (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.debug", false]], "default (sdcflows.config.loggers attribute)": [[5, "sdcflows.config.loggers.default", false]], "delta_te() (in module sdcflows.utils.phasemanip)": [[20, "sdcflows.utils.phasemanip.delta_te", false]], "denoiseimage (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.DenoiseImage", false]], "deoblique (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.Deoblique", false]], "deoblique_and_zooms() (in module sdcflows.utils.tools)": [[22, "sdcflows.utils.tools.deoblique_and_zooms", false]], "derivativesdatasink (class in sdcflows.workflows.outputs)": [[37, "sdcflows.workflows.outputs.DerivativesDataSink", false]], "disp_to_fmap() (in module sdcflows.transform)": [[15, "sdcflows.transform.disp_to_fmap", false]], "displacementsfield2fieldmap (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.DisplacementsField2Fieldmap", false]], "dry_run (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.dry_run", false]], "dumps() (in module sdcflows.config)": [[5, "sdcflows.config.dumps", false]], "ensure_positive_cosines() (in module sdcflows.utils.tools)": [[22, "sdcflows.utils.tools.ensure_positive_cosines", false]], "entities (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.entities", false]], "environment (class in sdcflows.config)": [[5, "sdcflows.config.environment", false]], "epi_mask() (in module sdcflows.utils.epimanip)": [[18, "sdcflows.utils.epimanip.epi_mask", false]], "estimatorregistry (class in sdcflows.utils.bimap)": [[17, "sdcflows.utils.bimap.EstimatorRegistry", false]], "estimatortype (class in sdcflows.fieldmaps)": [[7, "sdcflows.fieldmaps.EstimatorType", false]], "exec_docker_version (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.exec_docker_version", false]], "exec_env (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.exec_env", false]], "execution (class in sdcflows.config)": [[5, "sdcflows.config.execution", false]], "fieldmapestimation (class in sdcflows.fieldmaps)": [[7, "sdcflows.fieldmaps.FieldmapEstimation", false]], "fieldmapfile (class in sdcflows.fieldmaps)": [[7, "sdcflows.fieldmaps.FieldmapFile", false]], "fieldmapreportlet (class in sdcflows.interfaces.reportlets)": [[13, "sdcflows.interfaces.reportlets.FieldmapReportlet", false]], "file_path (in module sdcflows.config)": [[5, "sdcflows.config.file_path", false]], "find_anatomical_estimators() (in module sdcflows.utils.wrangler)": [[23, "sdcflows.utils.wrangler.find_anatomical_estimators", false]], "find_estimators() (in module sdcflows.utils.wrangler)": [[23, "sdcflows.utils.wrangler.find_estimators", false]], "find_meta (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.find_meta", false]], "fit() (sdcflows.transform.b0fieldtransform method)": [[15, "sdcflows.transform.B0FieldTransform.fit", false]], "flatten (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.Flatten", false]], "fmap_to_disp() (in module sdcflows.transform)": [[15, "sdcflows.transform.fmap_to_disp", false]], "fmapless (sdcflows.config.workflow attribute)": [[5, "sdcflows.config.workflow.fmapless", false]], "free_mem (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.free_mem", false]], "from_dict() (in module sdcflows.config)": [[5, "sdcflows.config.from_dict", false]], "front() (in module sdcflows.utils.misc)": [[19, "sdcflows.utils.misc.front", false]], "get() (in module sdcflows.config)": [[5, "sdcflows.config.get", false]], "get_free_mem() (in module sdcflows.utils.misc)": [[19, "sdcflows.utils.misc.get_free_mem", false]], "get_identifier() (in module sdcflows.fieldmaps)": [[7, "sdcflows.fieldmaps.get_identifier", false]], "get_key() (sdcflows.utils.bimap.estimatorregistry method)": [[17, "sdcflows.utils.bimap.EstimatorRegistry.get_key", false]], "get_linked_libs (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.get_linked_libs", false]], "get_plugin() (sdcflows.config.nipype class method)": [[5, "sdcflows.config.nipype.get_plugin", false]], "get_trt() (in module sdcflows.utils.epimanip)": [[18, "sdcflows.utils.epimanip.get_trt", false]], "get_workflow() (sdcflows.fieldmaps.fieldmapestimation method)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.get_workflow", false]], "getlogger() (sdcflows.config.loggers class method)": [[5, "sdcflows.config.loggers.getLogger", false]], "getreadouttime (class in sdcflows.interfaces.epi)": [[11, "sdcflows.interfaces.epi.GetReadoutTime", false]], "grid_bspline_weights() (in module sdcflows.transform)": [[15, "sdcflows.transform.grid_bspline_weights", false]], "init() (sdcflows.config.execution class method)": [[5, "sdcflows.config.execution.init", false]], "init() (sdcflows.config.loggers class method)": [[5, "sdcflows.config.loggers.init", false]], "init() (sdcflows.config.nipype class method)": [[5, "sdcflows.config.nipype.init", false]], "init_3dqwarp_wf() (in module sdcflows.workflows.fit.pepolar)": [[35, "sdcflows.workflows.fit.pepolar.init_3dQwarp_wf", false]], "init_brainextraction_wf() (in module sdcflows.workflows.ancillary)": [[27, "sdcflows.workflows.ancillary.init_brainextraction_wf", false]], "init_coeff2epi_wf() (in module sdcflows.workflows.apply.registration)": [[30, "sdcflows.workflows.apply.registration.init_coeff2epi_wf", false]], "init_fmap_derivatives_wf() (in module sdcflows.workflows.outputs)": [[37, "sdcflows.workflows.outputs.init_fmap_derivatives_wf", false]], "init_fmap_preproc_wf() (in module sdcflows.workflows.base)": [[31, "sdcflows.workflows.base.init_fmap_preproc_wf", false]], "init_fmap_reports_wf() (in module sdcflows.workflows.outputs)": [[37, "sdcflows.workflows.outputs.init_fmap_reports_wf", false]], "init_fmap_wf() (in module sdcflows.workflows.fit.fieldmap)": [[34, "sdcflows.workflows.fit.fieldmap.init_fmap_wf", false]], "init_magnitude_wf() (in module sdcflows.workflows.fit.fieldmap)": [[34, "sdcflows.workflows.fit.fieldmap.init_magnitude_wf", false]], "init_phdiff_wf() (in module sdcflows.workflows.fit.fieldmap)": [[34, "sdcflows.workflows.fit.fieldmap.init_phdiff_wf", false]], "init_sdcflows_wf() (in module sdcflows.workflows.fit.base)": [[33, "sdcflows.workflows.fit.base.init_sdcflows_wf", false]], "init_syn_preprocessing_wf() (in module sdcflows.workflows.fit.syn)": [[36, "sdcflows.workflows.fit.syn.init_syn_preprocessing_wf", false]], "init_syn_sdc_wf() (in module sdcflows.workflows.fit.syn)": [[36, "sdcflows.workflows.fit.syn.init_syn_sdc_wf", false]], "init_topup_wf() (in module sdcflows.workflows.fit.pepolar)": [[35, "sdcflows.workflows.fit.pepolar.init_topup_wf", false]], "init_unwarp_wf() (in module sdcflows.workflows.apply.correction)": [[29, "sdcflows.workflows.apply.correction.init_unwarp_wf", false]], "interface (sdcflows.config.loggers attribute)": [[5, "sdcflows.config.loggers.interface", false]], "last() (in module sdcflows.utils.misc)": [[19, "sdcflows.utils.misc.last", false]], "layout (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.layout", false]], "load() (in module sdcflows.config)": [[5, "sdcflows.config.load", false]], "load() (in module sdcflows.data)": [[6, "sdcflows.data.load", false]], "loader (class in sdcflows.data)": [[6, "sdcflows.data.Loader", false]], "local_hash_check (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.local_hash_check", false]], "log_dir (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.log_dir", false]], "log_level (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.log_level", false]], "loggers (class in sdcflows.config)": [[5, "sdcflows.config.loggers", false]], "main() (in module sdcflows.cli.main)": [[2, "sdcflows.cli.main.main", false]], "mapped (sdcflows.transform.b0fieldtransform attribute)": [[15, "sdcflows.transform.B0FieldTransform.mapped", false]], "match_histogram() (in module sdcflows.workflows.fit.syn)": [[36, "sdcflows.workflows.fit.syn.match_histogram", false]], "memory_gb (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.memory_gb", false]], "metadata (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.metadata", false]], "metadataerror": [[7, "sdcflows.fieldmaps.MetadataError", false]], "method (sdcflows.fieldmaps.fieldmapestimation attribute)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.method", false]], "module": [[1, "module-sdcflows.cli", false], [2, "module-sdcflows.cli.main", false], [3, "module-sdcflows.cli.parser", false], [4, "module-sdcflows.cli.workflow", false], [5, "module-sdcflows.config", false], [6, "module-sdcflows.data", false], [7, "module-sdcflows.fieldmaps", false], [8, "module-sdcflows.interfaces", false], [9, "module-sdcflows.interfaces.brainmask", false], [10, "module-sdcflows.interfaces.bspline", false], [11, "module-sdcflows.interfaces.epi", false], [12, "module-sdcflows.interfaces.fmap", false], [13, "module-sdcflows.interfaces.reportlets", false], [14, "module-sdcflows.interfaces.utils", false], [15, "module-sdcflows.transform", false], [16, "module-sdcflows.utils", false], [17, "module-sdcflows.utils.bimap", false], [18, "module-sdcflows.utils.epimanip", false], [19, "module-sdcflows.utils.misc", false], [20, "module-sdcflows.utils.phasemanip", false], [21, "module-sdcflows.utils.telemetry", false], [22, "module-sdcflows.utils.tools", false], [23, "module-sdcflows.utils.wrangler", false], [24, "module-sdcflows.viz", false], [25, "module-sdcflows.viz.utils", false], [26, "module-sdcflows.workflows", false], [27, "module-sdcflows.workflows.ancillary", false], [28, "module-sdcflows.workflows.apply", false], [29, "module-sdcflows.workflows.apply.correction", false], [30, "module-sdcflows.workflows.apply.registration", false], [31, "module-sdcflows.workflows.base", false], [32, "module-sdcflows.workflows.fit", false], [33, "module-sdcflows.workflows.fit.base", false], [34, "module-sdcflows.workflows.fit.fieldmap", false], [35, "module-sdcflows.workflows.fit.pepolar", false], [36, "module-sdcflows.workflows.fit.syn", false], [37, "module-sdcflows.workflows.outputs", false]], "nipype (class in sdcflows.config)": [[5, "sdcflows.config.nipype", false]], "nipype_version (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.nipype_version", false]], "notrack (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.notrack", false]], "nprocs (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.nprocs", false]], "omp_nthreads (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.omp_nthreads", false]], "output_dir (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.output_dir", false]], "overcommit_limit (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.overcommit_limit", false]], "overcommit_policy (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.overcommit_policy", false]], "padslices (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.PadSlices", false]], "parse_args() (in module sdcflows.cli.parser)": [[3, "sdcflows.cli.parser.parse_args", false]], "participant_label (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.participant_label", false]], "path (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.path", false]], "paths() (sdcflows.fieldmaps.fieldmapestimation method)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.paths", false]], "pdb (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.pdb", false]], "phasediff2fieldmap (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.Phasediff2Fieldmap", false]], "phasemap2rads (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.PhaseMap2rads", false]], "phdiff2fmap() (in module sdcflows.utils.phasemanip)": [[20, "sdcflows.utils.phasemanip.phdiff2fmap", false]], "plot_registration() (in module sdcflows.viz.utils)": [[25, "sdcflows.viz.utils.plot_registration", false]], "plugin (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.plugin", false]], "plugin_args (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.plugin_args", false]], "positivedirectioncosines (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.PositiveDirectionCosines", false]], "readable() (sdcflows.data.load method)": [[6, "sdcflows.data.load.readable", false]], "readable() (sdcflows.data.loader method)": [[6, "sdcflows.data.Loader.readable", false]], "remove_node_directories (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.remove_node_directories", false]], "reoblique (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.Reoblique", false]], "reorient_pedir() (in module sdcflows.utils.tools)": [[22, "sdcflows.utils.tools.reorient_pedir", false]], "reorientimageandmetadata (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.ReorientImageAndMetadata", false]], "resample_to_zooms() (in module sdcflows.utils.tools)": [[22, "sdcflows.utils.tools.resample_to_zooms", false]], "resource_monitor (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.resource_monitor", false]], "restore_env() (in module sdcflows.config)": [[5, "sdcflows.config.restore_env", false]], "run_uuid (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.run_uuid", false]], "sanitized_id (sdcflows.fieldmaps.fieldmapestimation attribute)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.sanitized_id", false]], "sdcflows.cli": [[1, "module-sdcflows.cli", false]], "sdcflows.cli.main": [[2, "module-sdcflows.cli.main", false]], "sdcflows.cli.parser": [[3, "module-sdcflows.cli.parser", false]], "sdcflows.cli.workflow": [[4, "module-sdcflows.cli.workflow", false]], "sdcflows.config": [[5, "module-sdcflows.config", false]], "sdcflows.data": [[6, "module-sdcflows.data", false]], "sdcflows.fieldmaps": [[7, "module-sdcflows.fieldmaps", false]], "sdcflows.interfaces": [[8, "module-sdcflows.interfaces", false]], "sdcflows.interfaces.brainmask": [[9, "module-sdcflows.interfaces.brainmask", false]], "sdcflows.interfaces.bspline": [[10, "module-sdcflows.interfaces.bspline", false]], "sdcflows.interfaces.epi": [[11, "module-sdcflows.interfaces.epi", false]], "sdcflows.interfaces.fmap": [[12, "module-sdcflows.interfaces.fmap", false]], "sdcflows.interfaces.reportlets": [[13, "module-sdcflows.interfaces.reportlets", false]], "sdcflows.interfaces.utils": [[14, "module-sdcflows.interfaces.utils", false]], "sdcflows.transform": [[15, "module-sdcflows.transform", false]], "sdcflows.utils": [[16, "module-sdcflows.utils", false]], "sdcflows.utils.bimap": [[17, "module-sdcflows.utils.bimap", false]], "sdcflows.utils.epimanip": [[18, "module-sdcflows.utils.epimanip", false]], "sdcflows.utils.misc": [[19, "module-sdcflows.utils.misc", false]], "sdcflows.utils.phasemanip": [[20, "module-sdcflows.utils.phasemanip", false]], "sdcflows.utils.telemetry": [[21, "module-sdcflows.utils.telemetry", false]], "sdcflows.utils.tools": [[22, "module-sdcflows.utils.tools", false]], "sdcflows.utils.wrangler": [[23, "module-sdcflows.utils.wrangler", false]], "sdcflows.viz": [[24, "module-sdcflows.viz", false]], "sdcflows.viz.utils": [[25, "module-sdcflows.viz.utils", false]], "sdcflows.workflows": [[26, "module-sdcflows.workflows", false]], "sdcflows.workflows.ancillary": [[27, "module-sdcflows.workflows.ancillary", false]], "sdcflows.workflows.apply": [[28, "module-sdcflows.workflows.apply", false]], "sdcflows.workflows.apply.correction": [[29, "module-sdcflows.workflows.apply.correction", false]], "sdcflows.workflows.apply.registration": [[30, "module-sdcflows.workflows.apply.registration", false]], "sdcflows.workflows.base": [[31, "module-sdcflows.workflows.base", false]], "sdcflows.workflows.fit": [[32, "module-sdcflows.workflows.fit", false]], "sdcflows.workflows.fit.base": [[33, "module-sdcflows.workflows.fit.base", false]], "sdcflows.workflows.fit.fieldmap": [[34, "module-sdcflows.workflows.fit.fieldmap", false]], "sdcflows.workflows.fit.pepolar": [[35, "module-sdcflows.workflows.fit.pepolar", false]], "sdcflows.workflows.fit.syn": [[36, "module-sdcflows.workflows.fit.syn", false]], "sdcflows.workflows.outputs": [[37, "module-sdcflows.workflows.outputs", false]], "send_crumb() (in module sdcflows.utils.telemetry)": [[21, "sdcflows.utils.telemetry.send_crumb", false]], "session_label (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.session_label", false]], "setup_migas() (in module sdcflows.utils.telemetry)": [[21, "sdcflows.utils.telemetry.setup_migas", false]], "sloppy (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.sloppy", false]], "sortpeblips (class in sdcflows.interfaces.epi)": [[11, "sdcflows.interfaces.epi.SortPEBlips", false]], "sources (sdcflows.fieldmaps.fieldmapestimation attribute)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.sources", false]], "sources (sdcflows.utils.bimap.estimatorregistry property)": [[17, "sdcflows.utils.bimap.EstimatorRegistry.sources", false]], "species (sdcflows.config.workflow attribute)": [[5, "sdcflows.config.workflow.species", false]], "stop_on_first_crash (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.stop_on_first_crash", false]], "subtract_phases() (in module sdcflows.utils.phasemanip)": [[20, "sdcflows.utils.phasemanip.subtract_phases", false]], "subtractphases (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.SubtractPhases", false]], "suffix (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.suffix", false]], "template_id (sdcflows.config.workflow attribute)": [[5, "sdcflows.config.workflow.template_id", false]], "templateflow_home (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.templateflow_home", false]], "templateflow_version (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.templateflow_version", false]], "to_displacements() (sdcflows.transform.b0fieldtransform method)": [[15, "sdcflows.transform.B0FieldTransform.to_displacements", false]], "to_filename() (in module sdcflows.config)": [[5, "sdcflows.config.to_filename", false]], "topupcoeffreorient (class in sdcflows.interfaces.bspline)": [[10, "sdcflows.interfaces.bspline.TOPUPCoeffReorient", false]], "total_memory (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.total_memory", false]], "transformcoefficients (class in sdcflows.interfaces.bspline)": [[10, "sdcflows.interfaces.bspline.TransformCoefficients", false]], "uniformgrid (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.UniformGrid", false]], "union (class in sdcflows.interfaces.brainmask)": [[9, "sdcflows.interfaces.brainmask.Union", false]], "unwarp_parallel() (in module sdcflows.transform)": [[15, "sdcflows.transform.unwarp_parallel", false]], "utils (sdcflows.config.loggers attribute)": [[5, "sdcflows.config.loggers.utils", false]], "version (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.version", false]], "work_dir (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.work_dir", false]], "worker() (in module sdcflows.transform)": [[15, "sdcflows.transform.worker", false]], "workflow (class in sdcflows.config)": [[5, "sdcflows.config.workflow", false]], "workflow (sdcflows.config.loggers attribute)": [[5, "sdcflows.config.loggers.workflow", false]], "write_graph (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.write_graph", false]]}, "objects": {"sdcflows": [[1, 0, 0, "-", "cli"], [5, 0, 0, "-", "config"], [6, 0, 0, "-", "data"], [7, 0, 0, "-", "fieldmaps"], [8, 0, 0, "-", "interfaces"], [15, 0, 0, "-", "transform"], [16, 0, 0, "-", "utils"], [24, 0, 0, "-", "viz"], [26, 0, 0, "-", "workflows"]], "sdcflows.cli": [[2, 0, 0, "-", "main"], [3, 0, 0, "-", "parser"], [4, 0, 0, "-", "workflow"]], "sdcflows.cli.main": [[2, 1, 1, "", "main"]], "sdcflows.cli.parser": [[3, 1, 1, "", "parse_args"]], "sdcflows.cli.workflow": [[4, 1, 1, "", "build_workflow"]], "sdcflows.config": [[5, 1, 1, "", "dumps"], [5, 2, 1, "", "environment"], [5, 2, 1, "", "execution"], [5, 5, 1, "", "file_path"], [5, 1, 1, "", "from_dict"], [5, 1, 1, "", "get"], [5, 1, 1, "", "load"], [5, 2, 1, "", "loggers"], [5, 2, 1, "", "nipype"], [5, 1, 1, "", "restore_env"], [5, 1, 1, "", "to_filename"], [5, 2, 1, "", "workflow"]], "sdcflows.config.environment": [[5, 3, 1, "", "cpu_count"], [5, 3, 1, "", "exec_docker_version"], [5, 3, 1, "", "exec_env"], [5, 3, 1, "", "free_mem"], [5, 3, 1, "", "nipype_version"], [5, 3, 1, "", "overcommit_limit"], [5, 3, 1, "", "overcommit_policy"], [5, 3, 1, "", "templateflow_version"], [5, 3, 1, "", "total_memory"], [5, 3, 1, "", "version"]], "sdcflows.config.execution": [[5, 3, 1, "", "ants_float"], [5, 3, 1, "", "bids_database_dir"], [5, 3, 1, "", "bids_database_wipe"], [5, 3, 1, "", "bids_description_hash"], [5, 3, 1, "", "bids_dir"], [5, 3, 1, "", "bids_filters"], [5, 3, 1, "", "cwd"], [5, 3, 1, "", "debug"], [5, 3, 1, "", "dry_run"], [5, 4, 1, "", "init"], [5, 3, 1, "", "layout"], [5, 3, 1, "", "log_dir"], [5, 3, 1, "", "log_level"], [5, 3, 1, "", "notrack"], [5, 3, 1, "", "output_dir"], [5, 3, 1, "", "participant_label"], [5, 3, 1, "", "pdb"], [5, 3, 1, "", "run_uuid"], [5, 3, 1, "", "session_label"], [5, 3, 1, "", "sloppy"], [5, 3, 1, "", "templateflow_home"], [5, 3, 1, "", "work_dir"], [5, 3, 1, "", "write_graph"]], "sdcflows.config.loggers": [[5, 3, 1, "", "cli"], [5, 3, 1, "", "default"], [5, 4, 1, "", "getLogger"], [5, 4, 1, "", "init"], [5, 3, 1, "", "interface"], [5, 3, 1, "", "utils"], [5, 3, 1, "", "workflow"]], "sdcflows.config.nipype": [[5, 3, 1, "", "crashfile_format"], [5, 3, 1, "", "get_linked_libs"], [5, 4, 1, "", "get_plugin"], [5, 4, 1, "", "init"], [5, 3, 1, "", "local_hash_check"], [5, 3, 1, "", "memory_gb"], [5, 3, 1, "", "nprocs"], [5, 3, 1, "", "omp_nthreads"], [5, 3, 1, "", "plugin"], [5, 3, 1, "", "plugin_args"], [5, 3, 1, "", "remove_node_directories"], [5, 3, 1, "", "resource_monitor"], [5, 3, 1, "", "stop_on_first_crash"]], "sdcflows.config.workflow": [[5, 3, 1, "", "analysis_level"], [5, 3, 1, "", "fmapless"], [5, 3, 1, "", "species"], [5, 3, 1, "", "template_id"]], "sdcflows.data": [[6, 2, 1, "", "Loader"], [6, 1, 1, "", "load"]], "sdcflows.data.Loader": [[6, 4, 1, "", "as_path"], [6, 4, 1, "", "cached"], [6, 4, 1, "", "readable"]], "sdcflows.data.load": [[6, 4, 1, "", "as_path"], [6, 4, 1, "", "cached"], [6, 4, 1, "", "readable"]], "sdcflows.fieldmaps": [[7, 2, 1, "", "EstimatorType"], [7, 2, 1, "", "FieldmapEstimation"], [7, 2, 1, "", "FieldmapFile"], [7, 6, 1, "", "MetadataError"], [7, 1, 1, "", "clear_registry"], [7, 1, 1, "", "get_identifier"]], "sdcflows.fieldmaps.FieldmapEstimation": [[7, 3, 1, "", "bids_id"], [7, 4, 1, "", "get_workflow"], [7, 3, 1, "", "method"], [7, 4, 1, "", "paths"], [7, 3, 1, "", "sanitized_id"], [7, 3, 1, "", "sources"]], "sdcflows.fieldmaps.FieldmapFile": [[7, 3, 1, "", "bids_root"], [7, 4, 1, "", "check_path"], [7, 3, 1, "", "entities"], [7, 3, 1, "", "find_meta"], [7, 3, 1, "", "metadata"], [7, 3, 1, "", "path"], [7, 3, 1, "", "suffix"]], "sdcflows.interfaces": [[9, 0, 0, "-", "brainmask"], [10, 0, 0, "-", "bspline"], [11, 0, 0, "-", "epi"], [12, 0, 0, "-", "fmap"], [13, 0, 0, "-", "reportlets"], [14, 0, 0, "-", "utils"]], "sdcflows.interfaces.brainmask": [[9, 2, 1, "", "BinaryDilation"], [9, 2, 1, "", "BrainExtraction"], [9, 2, 1, "", "Union"]], "sdcflows.interfaces.bspline": [[10, 2, 1, "", "ApplyCoeffsField"], [10, 2, 1, "", "BSplineApprox"], [10, 2, 1, "", "TOPUPCoeffReorient"], [10, 2, 1, "", "TransformCoefficients"], [10, 1, 1, "", "bspline_grid"]], "sdcflows.interfaces.epi": [[11, 2, 1, "", "GetReadoutTime"], [11, 2, 1, "", "SortPEBlips"]], "sdcflows.interfaces.fmap": [[12, 2, 1, "", "CheckB0Units"], [12, 2, 1, "", "CheckRegister"], [12, 2, 1, "", "DisplacementsField2Fieldmap"], [12, 2, 1, "", "PhaseMap2rads"], [12, 2, 1, "", "Phasediff2Fieldmap"], [12, 2, 1, "", "SubtractPhases"]], "sdcflows.interfaces.reportlets": [[13, 2, 1, "", "FieldmapReportlet"]], "sdcflows.interfaces.utils": [[14, 2, 1, "", "ConvertWarp"], [14, 2, 1, "", "DenoiseImage"], [14, 2, 1, "", "Deoblique"], [14, 2, 1, "", "Flatten"], [14, 2, 1, "", "PadSlices"], [14, 2, 1, "", "PositiveDirectionCosines"], [14, 2, 1, "", "Reoblique"], [14, 2, 1, "", "ReorientImageAndMetadata"], [14, 2, 1, "", "UniformGrid"]], "sdcflows.transform": [[15, 2, 1, "", "B0FieldTransform"], [15, 1, 1, "", "disp_to_fmap"], [15, 1, 1, "", "fmap_to_disp"], [15, 1, 1, "", "grid_bspline_weights"], [15, 1, 1, "", "unwarp_parallel"], [15, 1, 1, "", "worker"]], "sdcflows.transform.B0FieldTransform": [[15, 4, 1, "", "apply"], [15, 3, 1, "", "coeffs"], [15, 4, 1, "", "fit"], [15, 3, 1, "", "mapped"], [15, 4, 1, "", "to_displacements"]], "sdcflows.utils": [[17, 0, 0, "-", "bimap"], [18, 0, 0, "-", "epimanip"], [19, 0, 0, "-", "misc"], [20, 0, 0, "-", "phasemanip"], [21, 0, 0, "-", "telemetry"], [22, 0, 0, "-", "tools"], [23, 0, 0, "-", "wrangler"]], "sdcflows.utils.bimap": [[17, 2, 1, "", "EstimatorRegistry"], [17, 2, 1, "", "bidict"]], "sdcflows.utils.bimap.EstimatorRegistry": [[17, 4, 1, "", "get_key"], [17, 7, 1, "", "sources"]], "sdcflows.utils.bimap.bidict": [[17, 4, 1, "", "add"], [17, 4, 1, "", "clear"]], "sdcflows.utils.epimanip": [[18, 1, 1, "", "epi_mask"], [18, 1, 1, "", "get_trt"]], "sdcflows.utils.misc": [[19, 1, 1, "", "front"], [19, 1, 1, "", "get_free_mem"], [19, 1, 1, "", "last"]], "sdcflows.utils.phasemanip": [[20, 1, 1, "", "au2rads"], [20, 1, 1, "", "delta_te"], [20, 1, 1, "", "phdiff2fmap"], [20, 1, 1, "", "subtract_phases"]], "sdcflows.utils.telemetry": [[21, 1, 1, "", "send_crumb"], [21, 1, 1, "", "setup_migas"]], "sdcflows.utils.tools": [[22, 1, 1, "", "brain_masker"], [22, 1, 1, "", "deoblique_and_zooms"], [22, 1, 1, "", "ensure_positive_cosines"], [22, 1, 1, "", "reorient_pedir"], [22, 1, 1, "", "resample_to_zooms"]], "sdcflows.utils.wrangler": [[23, 1, 1, "", "find_anatomical_estimators"], [23, 1, 1, "", "find_estimators"]], "sdcflows.viz": [[25, 0, 0, "-", "utils"]], "sdcflows.viz.utils": [[25, 1, 1, "", "coolwarm_transparent"], [25, 1, 1, "", "plot_registration"]], "sdcflows.workflows": [[27, 0, 0, "-", "ancillary"], [28, 0, 0, "-", "apply"], [31, 0, 0, "-", "base"], [32, 0, 0, "-", "fit"], [37, 0, 0, "-", "outputs"]], "sdcflows.workflows.ancillary": [[27, 1, 1, "", "init_brainextraction_wf"]], "sdcflows.workflows.apply": [[29, 0, 0, "-", "correction"], [30, 0, 0, "-", "registration"]], "sdcflows.workflows.apply.correction": [[29, 1, 1, "", "init_unwarp_wf"]], "sdcflows.workflows.apply.registration": [[30, 1, 1, "", "init_coeff2epi_wf"]], "sdcflows.workflows.base": [[31, 1, 1, "", "init_fmap_preproc_wf"]], "sdcflows.workflows.fit": [[33, 0, 0, "-", "base"], [34, 0, 0, "-", "fieldmap"], [35, 0, 0, "-", "pepolar"], [36, 0, 0, "-", "syn"]], "sdcflows.workflows.fit.base": [[33, 1, 1, "", "init_sdcflows_wf"]], "sdcflows.workflows.fit.fieldmap": [[34, 1, 1, "", "init_fmap_wf"], [34, 1, 1, "", "init_magnitude_wf"], [34, 1, 1, "", "init_phdiff_wf"]], "sdcflows.workflows.fit.pepolar": [[35, 1, 1, "", "init_3dQwarp_wf"], [35, 1, 1, "", "init_topup_wf"]], "sdcflows.workflows.fit.syn": [[36, 1, 1, "", "init_syn_preprocessing_wf"], [36, 1, 1, "", "init_syn_sdc_wf"], [36, 1, 1, "", "match_histogram"]], "sdcflows.workflows.outputs": [[37, 2, 1, "", "DerivativesDataSink"], [37, 1, 1, "", "init_fmap_derivatives_wf"], [37, 1, 1, "", "init_fmap_reports_wf"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"], "5": ["py", "data", "Python data"], "6": ["py", "exception", "Python exception"], "7": ["py", "property", "Python property"]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:attribute", "4": "py:method", "5": "py:data", "6": "py:exception", "7": "py:property"}, "terms": {"": [5, 7, 10, 11, 12, 14, 15, 17, 18, 23, 29, 34, 35, 36, 37, 39, 41, 42, 44, 45], "0": [5, 7, 10, 12, 13, 14, 15, 18, 19, 20, 22, 25, 29, 34, 35, 36, 39, 41, 42, 44], "0001": [10, 22], "00017": 44, "00059": 18, "001": 5, "00119341": 18, "00246": 20, "00336": 44, "005": 7, "00522": 20, "006": 7, "00746": 7, "00768": 20, "008": 45, "01": [7, 23, 41], "011": 44, "0152472": 44, "01_dir": 7, "01_fieldmap": 7, "01_phase2": 7, "01_phasediff": 7, "01_t1w": 7, "02": 12, "02rad": 12, "03": 44, "04": 41, "05": [23, 41, 44], "05251": 18, "07": [41, 42], "08": [41, 44], "09": 41, "0rc1": 38, "1": [5, 7, 10, 12, 13, 14, 15, 17, 18, 19, 22, 23, 29, 34, 35, 36, 41, 42, 44, 45], "10": [10, 41, 44, 45], "100": [38, 45], "100185": 23, "1002": 44, "1006": 44, "101006": 23, "1016": 44, "102": 38, "10354": 44, "104": 38, "1054": 44, "108": 38, "1099": 44, "11": [5, 41, 44, 45], "1109": 44, "1115": 44, "112254_e9d6d38": 5, "1127": 44, "114": 38, "115": 38, "1156": 44, "116": 38, "1166": 44, "12": [15, 41, 45], "120": 38, "122": 38, "127": [18, 38], "128": 38, "13": [5, 41, 45], "130": 38, "131": 38, "132": 38, "133": 38, "137": 38, "1371": 44, "138": 38, "139": 44, "14": [41, 45], "142": 38, "143": 38, "149": 38, "1492": 44, "15": [5, 41, 45], "150": 38, "151": 38, "152": 38, "153": 38, "154": 38, "155": 38, "156": 38, "157": 38, "159": 38, "16": [5, 10, 39, 41, 42, 44, 45], "160": 38, "161": 38, "162": 38, "164": 38, "165": 38, "166": 38, "168": 38, "17": [10, 44, 45], "170": 38, "171": 44, "172": 38, "173": 38, "174": 38, "175": 38, "176": 38, "178": [38, 44], "18": [41, 45], "180": 38, "182": 38, "184": 38, "185": 38, "188": 38, "19": [44, 45], "190": 38, "191": 38, "1910340111": 44, "193": 44, "197": [38, 44], "199": 38, "1995": 44, "1997": 44, "199706": 44, "1999": 10, "1d": 15, "1ff15ecd54ac": 5, "1mm": 12, "2": [5, 10, 12, 14, 15, 17, 18, 23, 41, 42, 44, 45], "20": [10, 41, 44, 45], "200": [38, 45], "2000": 44, "2001": 44, "2002": 44, "2003": 44, "2004": 44, "2014": 44, "2016": 44, "2017": 44, "2019": 41, "202": 38, "2020": 41, "2021": 41, "2022": 41, "2023": 41, "20231129": 5, "2024": 41, "20241218": 5, "20261": 44, "204": 38, "205": 38, "207": 38, "209": 38, "21": [38, 45], "210": 38, "212": 38, "214": 38, "214420_48899722": 5, "215": [18, 38], "216": 38, "217": [38, 44], "22": [10, 41, 45], "2227266": 18, "223": 38, "224": 38, "228": 38, "229": 38, "23": [5, 41, 45], "230": 38, "234": 38, "237": 38, "239": 38, "24": [5, 41], "240": [38, 44], "243": 38, "247": 38, "248": 38, "25": [5, 41], "251": 38, "253": 38, "254": 38, "257": 38, "258": 38, "26": 41, "261": 38, "262": 38, "263": 38, "265": 38, "269": 38, "27": 41, "270": 38, "276": 38, "277": 38, "278": 38, "28": [12, 34, 38], "280": 38, "281": 38, "282": 38, "284": 38, "285": 38, "287": 38, "288": 38, "29": 41, "292": 38, "293": 38, "298": 38, "299": 38, "2d": 10, "2e6faa0": 38, "2ef64a92cec8": 5, "2pi": 38, "3": [9, 10, 14, 15, 17, 18, 22, 23, 36, 41, 42, 44, 45], "30": [25, 41], "301": 38, "302": 38, "303": 38, "304": 38, "308": 38, "309": 38, "310": 38, "311": 38, "312": 38, "313": 38, "314": 38, "315": 38, "317": 38, "319": 38, "321": 38, "322": 38, "324": 38, "326": 38, "327": 38, "329": 38, "334": 38, "335": 38, "337": 38, "3389": 44, "339": 38, "34": 44, "3408": 38, "341": 38, "342": 38, "343": 38, "346": 38, "348": 38, "349": 38, "35": 18, "351": 38, "354": 38, "355": 38, "356": 38, "358": 38, "35ff": 5, "36": [5, 23], "360": 38, "361cd67": 38, "364": 38, "366": 38, "367": 38, "368": 38, "371": 38, "374": 38, "375": 38, "379": 38, "38": 10, "380": 38, "381": 38, "387": 38, "39": 38, "390": 38, "391": 38, "393": 38, "394": 38, "396": 38, "398": 38, "399": 38, "3c171": 44, "3d": [10, 14, 44], "3dqwarp": [14, 35, 38, 44], "3e3": 44, "3mm": 36, "3t": 45, "4": [5, 14, 15, 17, 18, 22, 23, 41, 44, 45], "40": 10, "406": 38, "407": 38, "408": 38, "409": 38, "4096": 12, "41": 38, "410": 38, "411": 38, "412": 38, "415": 38, "417": 38, "418": 38, "419": 38, "42": 44, "420": 38, "421": 38, "424": 38, "425": 38, "426": 38, "427": 38, "428": 38, "429": 38, "43": 38, "431": 38, "434": 18, "436": 38, "44": 38, "440": 38, "444": 38, "449": 38, "449c2c2": 38, "45": 38, "450": [38, 44], "452": 38, "453": 38, "461": 44, "463e": 5, "47": 38, "48": [38, 45], "485e": 5, "49": [38, 44], "4d": [14, 15, 38], "4mm": 38, "5": [10, 15, 22, 23, 41, 42, 44, 45], "50": [5, 14, 38], "50mm": 12, "51": 38, "51573181152344": 5, "518": 38, "52": [38, 44], "53": 38, "55": 38, "56": 38, "57": 38, "576": 44, "58": 38, "59": 5, "5f": [18, 20], "6": [5, 10, 12, 15, 34, 41, 42, 44, 45], "60": 38, "606491088867188": 5, "61": 38, "62": 5, "63": 38, "65": 44, "7": [5, 13, 25, 41, 44, 45], "70": [38, 45], "717a69": 38, "73": 44, "7325": 18, "75": 38, "79": 38, "8": [5, 25, 39, 41, 45], "80": [38, 45], "8119": 44, "814": 44, "82": 38, "870": 44, "88": 38, "888": 44, "89": 38, "896788": 44, "9": [5, 18, 41, 42, 45], "90": [38, 45], "91": 38, "95": 38, "96": 38, "97": 38, "98": 38, "9f73": 5, "9f7e": 5, "A": [5, 6, 7, 10, 13, 14, 15, 17, 22, 23, 31, 34, 35, 36, 37, 38, 39, 42, 44], "As": [18, 38, 42], "By": [15, 44], "For": [6, 15, 18, 22, 23, 34, 44, 45], "If": [12, 14, 15, 18, 21, 23, 29, 36, 39, 44], "In": [10, 12, 15, 22, 38, 44, 45], "It": [6, 18, 44], "NOT": 38, "Not": 36, "ONE": 44, "On": [6, 42], "One": [23, 37, 44], "Such": 44, "That": [15, 45], "The": [5, 7, 9, 10, 12, 14, 15, 18, 22, 23, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44], "Then": [18, 44, 45], "There": 44, "These": [10, 23, 42, 44], "To": [14, 23, 38, 44], "With": [10, 18, 38], "_": [10, 17], "__spec__": 6, "__version__": 42, "_bold": 23, "_config": 5, "_dwi": 23, "_fieldmap": [12, 34], "_magnitud": 12, "_magnitude1": 12, "_magnitude2": 12, "_phase1": 12, "_phase2": 12, "_phasediff": 12, "_sbref": 23, "_t1w": 23, "_t2w": 23, "ab": 45, "about": [18, 38], "abov": [10, 34, 42, 45], "absenc": 44, "absolut": [18, 22, 38], "abstract": 13, "abstractcontextmanag": 6, "acc": 18, "acceler": [18, 44], "accept": [6, 22, 38], "access": [5, 6, 38, 41], "accordingli": 38, "account": [10, 18, 22, 44], "accur": [34, 35, 36, 38, 44], "accuraci": 18, "achiev": [15, 38], "acquir": [41, 44, 45], "acquisit": [18, 34, 41, 44], "acr": 6, "across": [5, 15, 35, 36, 38, 45], "action": [5, 38], "actual": [7, 10, 29, 34, 45], "ad": [10, 38], "adapt": [10, 38], "add": [0, 5, 14, 17, 38], "addit": [14, 22, 30, 42, 45], "addition": 38, "address": 38, "addtion": 38, "adebimp": 38, "adopt": 38, "advanc": 38, "affect": 38, "affili": 38, "affin": [6, 10, 12, 15, 38], "afni": [35, 42, 44], "after": [5, 9, 10, 14, 15, 23, 27, 29, 34, 35, 38], "afterward": 38, "aggreg": 39, "aid": [39, 44], "air": [22, 34, 45], "al": [10, 22, 44], "algorithm": [10, 38, 44], "align": [10, 15, 22, 30, 38, 44], "all": [5, 7, 10, 12, 14, 15, 17, 22, 23, 38, 39, 42, 45], "all_index": 45, "all_ndindex": 45, "all_ndindex_warp": 45, "allevi": 10, "alloc": 5, "allow": [5, 18, 23, 38, 39], "allow_neg": 15, "allowed_ent": 37, "along": [10, 18, 29, 38, 44, 45], "alpha": [13, 45], "alreadi": [5, 17, 34, 38, 44], "also": [6, 10, 23, 29, 36, 38, 39, 44], "alter": 38, "altern": [18, 44], "alwai": 10, "ambigu": 38, "amic": 38, "an": [5, 6, 9, 10, 11, 12, 13, 14, 15, 17, 18, 21, 22, 23, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 44, 45], "analys": 39, "analysi": [5, 39, 41, 44], "analysis_level": [0, 5, 39], "anat": [7, 23], "anat_fil": 23, "anat_mask": 36, "anat_nii": 25, "anat_ref": 36, "anat_suffix": 23, "anatom": [5, 23, 30, 34, 36, 37, 38, 44, 45], "anatomi": 45, "anchor": 6, "ancillari": [0, 26], "andersson": 44, "andersson2003": 44, "angl": 45, "ani": [5, 6, 11, 12, 14, 15, 23, 37, 44], "annoi": 38, "anoth": [10, 17], "ant": [5, 12, 14, 15, 30, 38, 39, 42, 44], "anterior": [36, 45], "ants_float": [0, 5], "antsapplytransform": [30, 44], "any_registr": 6, "any_registration_test": 6, "anymor": 10, "anyon": 38, "anyth": 38, "ap": 23, "apach": 38, "api": [38, 41, 44, 45], "app": 38, "appar": 45, "appli": [0, 10, 15, 23, 26, 34, 35, 36, 38, 44], "applic": [41, 44], "apply_mask": 13, "applycoeffsfield": [0, 10, 38], "appreci": 45, "approach": [7, 23, 38, 41], "appropri": [5, 29, 38], "approx": [10, 15, 18], "approxim": [10, 15, 36, 38, 45], "april": 41, "ar": [5, 6, 7, 10, 11, 12, 14, 15, 18, 22, 23, 34, 35, 36, 37, 38, 39, 41, 42, 44, 45], "arang": 45, "arbitrari": [20, 22], "arc": 18, "archiv": 38, "area": 36, "arg": [3, 5, 14, 17], "argument": [5, 7, 14, 23, 38, 41, 44], "argv": 2, "arm64": 38, "around": [18, 22, 25, 38, 45], "arrai": [15, 22, 44, 45], "art": 41, "artifact": [38, 44], "as_fil": 6, "as_path": [0, 6, 41], "asanyarrai": 45, "asl": [23, 38], "asr": 10, "assess": 18, "asset": 10, "assign": 39, "associ": [7, 15, 23, 36, 44], "assum": [12, 36, 44], "astyp": 45, "async": 15, "atla": [36, 38], "atlas_threshold": 36, "attach": 15, "attempt": [15, 23, 44, 45], "attribut": [7, 38], "au2rad": [0, 20], "august": 41, "auto": [25, 38, 45], "auto_": 23, "auto_00000": [17, 23], "auto_00001": [17, 23], "auto_00002": [17, 23], "auto_00003": 23, "auto_00004": 23, "auto_00005": 23, "auto_00006": 23, "auto_00007": 23, "auto_00008": 23, "auto_bold_nss": 36, "autofunct": 6, "autogener": 38, "autom": [5, 7, 44], "automat": [17, 23, 36, 39], "automethod": 6, "avail": [5, 6, 7, 11, 18, 23, 38, 39, 42, 44], "averag": [34, 36, 38, 44], "avoid": [14, 38], "ax": [10, 14, 15, 22, 38, 44, 45], "axcodes2ornt": 22, "axes_grid1": 45, "axi": [10, 14, 15, 44, 45], "axial": [25, 45], "axin": 45, "axis_cbar": 45, "azeez": 38, "b": [10, 15, 17, 22, 23, 27, 29, 34, 35, 36, 38, 44], "b0": [12, 41], "b0field": 38, "b0fieldidentifi": [7, 23, 31, 37, 38, 41], "b0fieldsourc": 38, "b0fieldtransform": [0, 10, 15, 38, 41], "b1": 34, "b_0": [10, 15, 18, 34, 38, 44, 45], "back": [23, 34, 38], "background": 25, "backport": 38, "bad": 38, "balaban": 44, "ball": 9, "bandwidth": 45, "base": [0, 5, 7, 9, 10, 11, 12, 13, 14, 15, 17, 26, 32, 34, 35, 36, 37, 41, 42, 44], "base_directori": 37, "base_ent": 23, "basenam": 38, "basi": [15, 38, 44], "basic": [19, 23, 45], "basil": 38, "batteri": 37, "bbox_to_anchor": 45, "bbox_transform": 45, "becaus": [10, 18, 23, 44], "becom": 45, "been": [5, 18, 23, 38, 44], "befor": [5, 15, 38], "beginn": 45, "behavior": 38, "behind": 44, "being": [6, 38, 41], "believ": 18, "below": [36, 44, 45], "berlin": 44, "besid": 34, "best": 10, "bet": 38, "beta": 15, "better": [7, 18, 38], "between": [10, 44], "beyond": 10, "bid": [5, 7, 11, 12, 18, 20, 23, 34, 37, 38, 41], "bidict": [0, 17], "bidirect": 17, "bids_database_dir": [0, 5], "bids_database_wip": [0, 5], "bids_description_hash": [0, 5], "bids_dir": [0, 5, 39], "bids_filt": [0, 5, 23], "bids_fmap_id": 37, "bids_id": [0, 7, 23, 38], "bids_root": [0, 7], "bidsfil": 23, "bidslayout": [5, 23], "bimap": [0, 16], "binari": [9, 14, 34, 42], "binarydil": [0, 9], "biom": 44, "bioscienc": 38, "bit": 18, "black": 45, "blair": 38, "blip": [11, 38], "blob": 39, "blocksiz": 38, "blue": 45, "blur": 15, "bodi": 10, "boilerpl": 38, "bold": [10, 23, 36, 38, 44], "boldref": 38, "bool": [7, 15, 21, 23, 29, 30, 31, 34, 35, 36, 37], "boolean": [10, 12, 13, 14, 37], "border": 15, "bore": 45, "both": [12, 13, 22, 38, 44], "bottom": 45, "bound": [15, 39], "boundari": [7, 10], "brain": [9, 10, 12, 13, 18, 27, 30, 34, 36, 37, 38, 40, 41, 44], "brain_cmap": 45, "brain_mask": [0, 22], "brain_slic": 45, "brainextract": [0, 9], "brainextraction_wf": 27, "brainmask": [0, 8, 27, 36], "branch": 38, "breadcrumb": 21, "break": 38, "bring": 38, "bs_space": 10, "bspline": [0, 8, 38, 44], "bspline_dist": 27, "bspline_grid": [0, 10], "bsplineapprox": [0, 10, 38], "bug": 38, "bugfix": 38, "build": [4, 7, 33, 36, 37, 38, 42, 44], "build_workflow": [0, 4, 5], "built": [5, 23, 44], "bump": 38, "byte": [14, 23], "c": [10, 15, 17, 42, 45], "cach": [0, 5, 6, 15, 38, 39, 41], "caclul": 38, "calcul": [10, 11, 12, 15, 18, 20, 27, 29, 31, 34, 36, 38, 44, 45], "call": [5, 6, 7, 10, 15, 17, 18, 20, 21, 29, 38], "callabl": [6, 15], "can": [5, 7, 10, 14, 15, 18, 22, 23, 30, 34, 39, 42, 44, 45], "candid": [23, 44], "cannot": 17, "capabl": 14, "captur": 38, "cardin": [10, 38], "carri": 15, "case": [6, 10, 12, 23, 30, 38, 44, 45], "cast": 38, "caus": 15, "caution": 44, "cax": 45, "cbar": 45, "cdot": [15, 18, 44], "center": [10, 18, 38, 45], "centerednorm": 45, "central": 38, "chang": [14, 23, 39, 41], "channel": [13, 44], "charact": [7, 38], "character": 44, "cheapli": 38, "check": [3, 5, 12, 14, 38, 42], "check_hdr": 37, "check_path": [0, 7], "checkb0unit": [0, 12], "checkregist": [0, 12], "checksum": 5, "choic": [38, 39], "choke": 38, "choos": [5, 38], "christoph": 38, "ci": 38, "cieslak": 38, "circl": 38, "circleci": 38, "citizen": 38, "class": [0, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 17, 37], "classmethod": 5, "clean": [6, 23], "cleanup": 38, "clear": [0, 17, 44], "clear_registri": [0, 7, 23, 41], "cli": [0, 5, 38, 41], "client": [5, 21], "clip": [27, 44], "close": [15, 45], "cluster": 39, "cmap": 45, "cnr": 38, "co": [36, 44], "code": [5, 10, 14, 29, 30, 34, 35, 36, 38], "codecov": 38, "codespel": 38, "coeff": [0, 15], "coeff2epi": 38, "coeff2epi_wf": [30, 38], "coeffici": [10, 15, 29, 30, 31, 34, 35, 36, 37, 38, 44], "coerc": 37, "cognit": 38, "collat": 38, "collect": [5, 7, 38], "colleg": 38, "collis": 38, "coloc": 38, "color": [25, 45], "colorbar": 45, "colormap": 45, "com": 39, "combin": [15, 31], "come": [23, 45], "command": [2, 3, 5, 14, 41, 42], "comment": 38, "commissur": 45, "commit": 38, "commun": 21, "compact": [15, 44], "compat": [14, 15, 38, 44], "complet": 38, "compliant": [5, 39], "complic": [23, 44], "compon": 44, "comprehens": [23, 38], "compress": [25, 37, 38], "comput": [5, 14, 15, 36], "concaten": 38, "concurr": 38, "conda": 38, "conduc": 38, "config": [0, 38, 39, 41], "config_fil": [4, 5], "configur": [0, 14, 15, 30, 35, 36, 39, 41], "confus": [18, 38], "connect": 38, "consecut": 34, "consid": 38, "consist": [5, 7, 11, 12, 14, 38, 44], "consol": 18, "constant": [15, 45], "constraint": 38, "construct": 38, "consum": 14, "consumpt": 5, "contain": [5, 6, 15, 17, 23, 34, 35, 37, 38, 44], "content": 6, "context": [6, 38], "continu": [5, 38, 44, 45], "contour": 25, "contrast": [6, 36], "contribut": 38, "contributor": 38, "control": [10, 15, 30], "control_zooms_mm": 10, "conveni": 5, "convent": 11, "convers": [5, 35, 36, 38], "convert": [12, 14, 15, 20, 34, 38, 44], "convertwarp": [0, 14], "coolwarm": 25, "coolwarm_transpar": [0, 25], "coordin": [10, 14, 15, 22, 44], "copi": [5, 6, 14, 38, 45], "copy_head": 14, "copyheaderinterfac": 14, "copyright": 38, "core": 34, "coregistr": 44, "cornerston": 44, "coron": 25, "correct": [0, 10, 14, 15, 28, 34, 38, 41, 44], "corrected_mask": 29, "correctli": [23, 38], "correspond": [5, 7, 10, 11, 12, 14, 23, 29, 30, 34, 35, 36, 38, 41, 44, 45], "cosin": [10, 14, 22], "cost": [36, 44, 45], "cover": [22, 38], "coverag": 38, "cox": 44, "cox1997": 44, "cpu": [5, 35, 36, 38, 39], "cpu_count": [0, 5], "crashfil": 5, "crashfile_format": [0, 5], "crawl": 5, "creat": [4, 5, 6, 10, 15, 23, 31, 33, 35, 36, 38], "ctrl_nii": 15, "cubic": [10, 15], "current": [5, 39], "custom": [5, 39], "custom_ent": 37, "cut": 25, "cval": 15, "cwd": [0, 5], "cyceron": 38, "d": [10, 14, 17, 38], "d20231128": 5, "d_": 44, "data": [0, 5, 7, 9, 10, 11, 14, 15, 18, 22, 23, 37, 38, 40, 41], "data2fmap_xfm": 10, "data_dtyp": 37, "databas": [5, 39], "datalad": 38, "dataobj": 45, "dataset": [5, 10, 14, 15, 23, 29, 30, 33, 35, 37, 38, 39, 41], "dataset_descript": 5, "datasink": 37, "datatyp": 37, "date": 38, "deal": [11, 12], "debian": 42, "debug": [0, 5, 10, 29, 30, 31, 34, 35, 36, 38, 39], "debugg": [5, 39], "decemb": 41, "decim": 10, "dedupl": 38, "deep": 38, "def": 45, "default": [0, 5, 9, 10, 12, 13, 14, 15, 25, 27, 31, 34, 37, 38, 39, 44], "defin": [37, 44, 45], "deform": [15, 36, 44], "degre": 15, "del": 17, "delet": 6, "delimit": 39, "delta": [34, 44, 45], "delta_": [18, 20, 44], "delta_t": [0, 20], "demean": [12, 38], "denoiseimag": [0, 14], "dens": 38, "deobliqu": [0, 14, 44], "deoblique_and_zoom": [0, 22], "depart": 38, "depend": [31, 38, 41], "deploi": [38, 42], "deploy": 38, "deprec": 38, "dept": 38, "deriv": [5, 15, 31, 37, 38, 41, 44], "derivativesdatasink": [0, 37, 38], "desc": 45, "describ": [5, 14, 38, 39, 44, 45], "descript": [5, 34, 35, 36, 38, 42], "design": [15, 38, 41, 45], "detach": 38, "detail": [38, 44], "detect": [36, 38], "determin": [10, 15, 22, 29], "dev0": 5, "dev5": 5, "develop": [5, 38, 39, 41, 44], "deviat": 45, "devic": [38, 45], "diagon": 10, "dict": [5, 17, 20, 21, 23, 34, 35, 36, 37], "dictionari": [5, 11, 12, 14, 17, 23, 29, 35, 36, 37], "diff": 12, "differ": [7, 12, 18, 20, 23, 34, 38, 41], "diffus": [23, 44], "dilat": 9, "dimens": [10, 14, 15], "dimension": [14, 44], "dir": [5, 39], "direct": [10, 11, 12, 14, 18, 22, 23, 35, 36, 38, 41], "directli": [6, 10, 15, 34, 38, 44], "director": 10, "directori": [5, 6, 31, 37, 39], "disabl": [5, 7], "disappear": 18, "discov": [38, 41], "discret": 45, "discuss": [18, 44], "disk": 5, "dismiss": [15, 23], "dismiss_ent": 37, "disp_to_fmap": [0, 15, 41], "displac": [12, 14, 15, 29, 36, 38, 44, 45], "displacementsfield2fieldmap": [0, 12], "displai": 41, "distanc": [27, 38], "distinct": 38, "distort": [10, 15, 23, 29, 30, 36, 38, 40, 41], "distortedref": 38, "distribut": [6, 10], "div_id": 25, "divid": [38, 44], "dmriprep": 38, "do": [5, 6, 15, 18, 38, 44], "doc": [5, 38, 39], "docker": [5, 38], "dockerfil": 42, "docstr": [6, 38], "document": [6, 18, 38, 45], "doe": [5, 10, 15, 18, 38], "doi": 44, "done": [18, 34, 38], "dot": [38, 45], "dotsb": [34, 44], "doubl": 38, "download": 38, "downsampl": 38, "downstream": 38, "dr": 18, "drift": 44, "driven": 44, "drop": [5, 15, 38], "dry": [38, 39], "dry_run": [0, 5], "ds000054": 23, "ds000206": 23, "ds001600": 23, "ds001771": [23, 38], "dsa": 23, "dsa_dir": 7, "dsb": 23, "dsc": 23, "dseg": 38, "dtype": [15, 37, 45], "due": 38, "dump": [0, 5, 41], "duplic": 6, "durat": 6, "dure": 38, "dwi": [10, 23, 38, 44], "dynam": 38, "e": [5, 10, 12, 15, 17, 18, 22, 36, 37, 38, 39, 45], "e0152472": 44, "e3b6": 5, "e_i": 45, "e_j": 45, "each": [5, 10, 15, 35, 39, 45], "earli": [5, 18], "eas": 44, "easili": [5, 15, 41], "ec": 45, "echo": [18, 34, 38, 41, 44, 45], "echospac": 18, "echotim": [7, 34], "echotime1": [20, 34], "echotime2": [7, 20, 34], "echotimediffer": 20, "edg": 45, "edgecolor": 45, "educ": 45, "ee": 18, "effect": [10, 18, 38, 40, 41, 44], "effectiveechospac": 18, "effici": [6, 38], "effigi": 38, "eilidh": 38, "either": [5, 10, 34], "elaps": 44, "element": [9, 19, 35, 36, 45], "elif": 45, "elsewher": 34, "embed": [10, 15], "emploi": 14, "empric": 38, "empti": [7, 14, 17, 23, 45], "enabl": [5, 7, 10, 31, 38, 39], "encod": [10, 12, 15, 23, 35, 36, 38, 44, 45], "encount": 5, "enforc": 38, "engin": [5, 18], "enh": 38, "enhanc": [38, 44], "enlist": 5, "enough": 18, "ensur": [6, 12, 14, 34, 38], "ensure_positive_cosin": [0, 22], "enter": 6, "enthusiast": 44, "entiti": [0, 7, 23, 37, 38, 39], "entri": 2, "enum": 7, "environ": [0, 5, 14, 41, 42], "epi": [0, 8, 9, 10, 12, 14, 15, 18, 22, 23, 27, 29, 30, 35, 36, 38, 41, 44, 45], "epi_mask": [0, 18, 36], "epi_nii": 15, "epi_ref": 36, "epifactor": 18, "epimanip": [0, 16], "eq": [10, 15, 18, 44], "eqref": [15, 18, 44], "equal": 39, "equival": [18, 34, 44], "error": [5, 7, 10, 18, 38, 44], "especi": [39, 44], "esteban": [38, 44], "esteban2016": 44, "estim": [2, 3, 5, 7, 10, 14, 15, 17, 23, 27, 30, 31, 33, 34, 35, 36, 37, 38, 39, 41, 45], "estimate_bright": 25, "estimatorregistri": [0, 17], "estimatortyp": [0, 7, 23, 41], "et": [10, 44], "etc": [5, 18, 38, 45], "evad": 38, "evalu": [10, 15, 38, 44], "even": [10, 14], "everi": [5, 10, 15, 44], "evid": 12, "exactli": 45, "exagger": 38, "exampl": [5, 7, 17, 19, 20, 23, 41], "except": [5, 7, 23, 39], "exclud": 36, "exclus": [10, 14, 23], "exec_docker_vers": [0, 5], "exec_env": [0, 5], "execut": [0, 2, 3, 4, 5, 14, 15, 23, 36, 39, 41, 44, 45], "exercis": 38, "exist": [5, 6, 9, 10, 11, 12, 13, 14, 37, 39, 44], "exit": [6, 39], "exit_p": 21, "expans": 38, "expect": [6, 12, 14, 36, 38], "experiment": 44, "explicit": [6, 41], "exploit": 44, "export": 5, "expos": 38, "express": [15, 44], "ext": 6, "extend": 15, "extens": 38, "extent": [15, 22, 45], "extern": 41, "extra": [10, 37], "extract": [7, 9, 14, 27, 37, 38], "extrapol": [10, 15, 38], "extrem": [22, 38], "extremelli": 45, "ey": 38, "f": [7, 10, 15, 18, 20, 38], "f_": 18, "fact": 44, "factor": [10, 14, 18, 22, 34, 44], "factor_tol": 22, "fail": 38, "failur": 38, "fairli": 45, "fall": [15, 45], "fals": [5, 6, 7, 10, 12, 13, 14, 15, 23, 25, 29, 30, 31, 34, 35, 36, 37, 39, 45], "fast": [29, 30, 34, 35, 36, 38, 44, 45], "faster": [31, 39], "fastest": 45, "fat": 18, "fc": 45, "featur": 38, "februari": 41, "fed": [11, 35, 44], "feed": 10, "feedback": 44, "few": 23, "fewer": 44, "fiddl": 38, "field": [7, 10, 12, 14, 15, 18, 23, 29, 30, 31, 34, 35, 36, 37, 38, 44], "fieldcoeff": [10, 38], "fieldmap": [0, 2, 3, 5, 10, 11, 12, 13, 15, 17, 20, 23, 27, 29, 30, 31, 32, 35, 36, 37, 38, 39, 41, 45], "fieldmapestim": [0, 7, 17, 23, 31, 38, 41], "fieldmapfil": [0, 7, 23, 38, 41], "fieldmapless": 38, "fieldmapreportlet": [0, 13, 38], "fieldwarp": [29, 38], "fig": [44, 45], "figsiz": 45, "figur": 45, "file": [5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 23, 27, 30, 35, 36, 37, 38, 39, 42], "file1": 17, "file2": 17, "file3": 17, "file4": 17, "file5": 17, "file_path": [0, 5, 41], "filenam": [5, 7, 13, 14, 37, 38], "filepath": 7, "filesystem": [5, 6], "fill": 45, "filter": [5, 10, 15, 23, 38, 39, 44], "final": [15, 23, 38, 41], "find": [10, 18, 23, 38, 39, 44], "find_anatomical_estim": [0, 23], "find_estim": [0, 23, 44], "find_meta": [0, 7], "fine": 38, "first": [5, 10, 14, 18, 35, 36, 38, 44], "fit": [0, 10, 15, 26, 38, 44], "fix": [37, 38, 44], "fixat": 10, "fixed_hdr": 37, "fixup": 38, "flag": [7, 38], "flake8": 38, "flat": 5, "flatten": [0, 14, 17, 35], "fledg": 10, "flexibil": 38, "flexibl": [6, 44], "flexibli": 38, "flirt": 38, "flirtsch": 6, "float": [5, 9, 10, 11, 12, 13, 15, 22, 36, 38], "float32": [15, 45], "float64": 15, "flow": 38, "fm": 23, "fmap": [0, 6, 7, 8, 30, 31, 34, 35, 36], "fmap2data_xfm": 10, "fmap_atla": 6, "fmap_atlas_2_mni152nlin2009casym_affin": 6, "fmap_coeff": [29, 30, 31, 34, 35, 36, 37], "fmap_derivatives_wf": 37, "fmap_fil": 12, "fmap_hz": 15, "fmap_mask": [30, 34, 35, 37], "fmap_nii": 15, "fmap_preproc_wf": 31, "fmap_ref": [10, 30, 31, 34, 35, 36, 37], "fmap_reports_wf": 37, "fmap_target": 10, "fmap_to_disp": [0, 15, 41], "fmap_typ": 37, "fmap_wf": 34, "fmapid": 38, "fmapless": [0, 5, 23, 39, 44], "fmri": 44, "fmriprep": [23, 38], "fninf": 44, "focu": 45, "focus": 38, "folder": [5, 39, 44], "follow": [6, 10, 15, 18, 22, 38, 42, 44], "fontsiz": 45, "footprint": 39, "forc": [5, 14, 23, 39, 44], "force_fmapless": [23, 44], "foreground": [25, 38], "fork": 38, "forkserv": 5, "form": [10, 14, 15, 22, 38], "formal": [10, 15], "format": [5, 15, 29, 44], "formul": [10, 18], "formula": 45, "forward": 38, "found": [18, 23, 38, 39, 42, 44], "four": 23, "fourth": 15, "fov": [12, 38, 45], "frac": [18, 44], "framework": [15, 38, 44], "franc": 38, "free": [5, 19], "free_mem": [0, 5, 29], "freedom": 15, "freeli": 44, "freesurf": [5, 42], "freie": 44, "frequenc": 18, "from": [5, 6, 7, 10, 11, 12, 14, 15, 18, 19, 20, 22, 23, 27, 29, 34, 36, 37, 38, 39, 42, 44, 45], "from_dict": [0, 5, 41], "from_fil": [9, 10, 11, 12, 14], "front": [0, 19, 38, 44], "fsl": [10, 11, 18, 34, 35, 38, 42, 44], "full": [6, 15, 25], "fulldataset": 15, "fulli": [6, 10, 22], "func": [6, 15], "function": [0, 5, 6, 15, 22, 23, 36, 38, 42, 44], "fund": 39, "furo": 38, "further": [3, 18, 44], "furtherr": 45, "fuse": 45, "g": [5, 10, 12, 18, 36, 37, 38, 39, 45], "gaa86b0b08f": 5, "gamma": [18, 44], "gaussian": 14, "gb": [5, 39], "gener": [6, 10, 12, 13, 15, 17, 22, 30, 31, 34, 38, 45], "geometr": 44, "get": [0, 5, 17, 18, 38, 41, 45], "get_cent": 45, "get_data": 38, "get_fdata": [38, 45], "get_free_mem": [0, 19], "get_identifi": [0, 7, 41], "get_kei": [0, 17], "get_linked_lib": [0, 5], "get_plugin": [0, 5], "get_trt": [0, 18], "get_workflow": [0, 7], "getlogg": [0, 5], "getreadouttim": [0, 11], "getter": 6, "gh": 38, "git": 38, "github": [38, 39], "given": [5, 7, 12, 15, 20, 23, 27, 29, 35, 36, 38, 39, 44, 45], "goncalv": 38, "gone": 10, "gorgolewski": 38, "govern": 45, "gradient": 44, "grai": 45, "graph": [4, 5, 29, 30, 34, 35, 36, 38], "grappa": 18, "grayscal": [18, 22, 45], "gre": [9, 27, 34, 44], "greater": [6, 39], "grid": [10, 15, 22, 29, 35, 38, 45], "grid_bspline_weight": [0, 10, 15, 41], "grid_refer": 35, "ground": 45, "group": [22, 38, 39], "gt": 15, "guid": [18, 34], "guidelin": 38, "gyromagnet": [18, 44], "gz": [6, 7, 12, 18, 34, 45], "h": [38, 39, 44], "ha": [5, 10, 15, 18, 22, 23, 38, 44, 45], "habitu": 42, "had": 38, "handl": [15, 38, 41, 42], "happen": [5, 15, 45], "hard": [5, 38], "harvard": 38, "hashmap": 17, "have": [5, 10, 12, 14, 15, 22, 23, 25, 34, 35, 36, 38, 44, 45], "hcp": [23, 38], "hcp101006": 23, "hcph": 5, "head": [10, 15, 29], "header": [10, 14, 37, 38], "hear": 38, "height": 45, "held": 18, "help": [39, 45], "henc": 10, "here": [10, 15, 18, 22, 44], "heurist": [5, 23, 38, 44], "hi": 18, "high": [38, 44], "higher": [38, 44], "histogram": [36, 44], "histori": 38, "hmc": [10, 15], "hmc_xfm": 15, "hmc_xform": 29, "home": [5, 39], "homogen": 38, "horizont": 45, "hospit": 38, "host": 38, "hot": 38, "hotfix": 38, "housekeep": 38, "how": [15, 18, 23, 42, 44, 45], "howev": [39, 45], "hpc": 39, "http": 39, "human": 5, "huntenburg": 44, "huntenburg2014": 44, "hutton": 44, "hutton2002": 44, "hz": [12, 13, 15, 20, 29, 34, 37, 38, 44], "i": [5, 6, 7, 10, 11, 12, 14, 15, 17, 18, 21, 22, 23, 25, 30, 34, 36, 38, 39, 41, 42, 44], "id": 5, "idea": 38, "ident": [22, 38], "identifi": [5, 7, 15, 23, 38, 39, 44], "ieee": [10, 44], "ignor": 38, "ij": 45, "im": 45, "imag": [10, 11, 12, 14, 15, 18, 22, 23, 27, 29, 30, 34, 36, 38, 41, 45], "imagingfrequ": 18, "img": [10, 18, 22], "img_mask": 36, "immedi": 38, "impact": 38, "implement": [5, 6, 10, 15, 18, 38, 41], "implicit": 41, "import": [5, 6, 22, 23, 38, 42, 45], "importlib": 6, "importlib_resourc": 6, "impos": 45, "improv": [6, 38, 39], "imshow": 45, "in1": 9, "in2": 9, "in_": 31, "in_anat": 36, "in_coeff": 10, "in_data": [10, 11, 14, 35], "in_epi": [14, 36], "in_field": 14, "in_fil": [9, 11, 12, 14, 18, 20, 22, 27, 37], "in_mask": [10, 14], "in_meta": [12, 14, 18, 20, 36], "in_orient": 14, "in_phas": [12, 20], "in_plumb": 14, "in_refer": 22, "in_valu": 20, "in_xfm": 10, "includ": [6, 15, 23, 38, 39, 44], "inclus": 23, "incomplet": 38, "inconsist": 38, "incorpor": 38, "incorrect": 38, "increas": [22, 38, 39], "incub": 38, "inde": 45, "independ": [15, 39], "index": [5, 7, 14, 15, 35, 39, 45], "indic": [5, 7, 14, 23, 39], "indicate_inset_zoom": 45, "individu": [29, 30, 31, 34, 44], "induc": 38, "infer": [7, 14], "inform": [0, 5, 38, 39, 44], "infrastructur": 38, "inhomogen": [29, 44], "init": [0, 5, 21], "init_3dqwarp_wf": [0, 35], "init_brainextraction_wf": [0, 27], "init_coeff2epi_wf": [0, 30], "init_fmap_derivatives_wf": [0, 37], "init_fmap_preproc_wf": [0, 31, 38], "init_fmap_reports_wf": [0, 37], "init_fmap_wf": [0, 34], "init_magnitude_wf": [0, 34], "init_p": 21, "init_phdiff_wf": [0, 34], "init_sdcflows_wf": [0, 33], "init_syn_preprocessing_wf": [0, 36, 44], "init_syn_sdc_wf": [0, 36, 44], "init_topup_wf": [0, 35, 38], "init_unwarp_wf": [0, 29], "initi": [5, 7, 21, 23, 38], "inlin": [38, 45], "inlist": 19, "input": [5, 7, 9, 10, 11, 12, 13, 14, 15, 20, 22, 23, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 44], "input_imag": 14, "insert": [17, 38, 45], "inset": 45, "inset_ax": 45, "inset_loc": 45, "insid": 45, "inspect": 12, "instal": [5, 38, 41], "instanc": [7, 22, 23, 38, 39, 44], "instead": [15, 38], "instrument": 41, "int": [15, 22, 27, 29, 30, 31, 34, 35, 36, 45], "inted": 38, "integ": [10, 14, 27, 44], "integr": [38, 44], "intend": [6, 14], "intendedfor": [7, 23, 38, 41], "intens": [36, 38, 44], "intensityclip": 38, "intent": [38, 44], "interact": 38, "interfac": [5, 6, 7, 22, 38, 39, 41, 44], "intermedi": [5, 39], "intern": [15, 35, 36, 38], "interpol": [10, 15, 29, 38, 44], "interpret": [6, 42, 44], "intersphinx": 38, "intramodalmerg": 38, "introduc": [15, 38, 44], "inu": 38, "invers": [15, 22, 36], "invert": [22, 38], "investig": 23, "is_in_fov": 45, "ishandl": 38, "isol": 38, "issu": [5, 38, 45], "item": [10, 11, 12, 14, 17, 37], "iter": 15, "itertool": 45, "itk": [12, 14, 15, 29, 30], "itk_format": 15, "itk_transform": 12, "its": [10, 29, 34, 37, 44], "j": [10, 11, 12, 14, 15, 18, 22, 38, 44], "j_axi": 45, "jacobian": [10, 15, 29, 38], "januari": 41, "jenkinson": 44, "jenkinson2003": [34, 44], "jezzard": 44, "jezzard1995": 44, "job": 39, "join": 5, "joinpath": 6, "journal": 44, "json": [5, 6, 7, 18, 39], "juli": 41, "june": 41, "jupyt": 38, "just": [5, 10, 15, 27, 34], "k": [10, 11, 12, 14, 15, 22, 44, 45], "k_1": 15, "k_2": 15, "k_3": 15, "keep": [5, 38], "kei": [11, 12, 14, 17, 23, 37, 38], "kernel": [5, 15, 38], "kevin": 38, "keyerror": 17, "keyserv": 38, "keyword": 7, "king": 38, "knot": 15, "known": [10, 18], "krzysztof": 38, "kwarg": [7, 13, 17, 21], "l": 44, "la": 22, "label": [13, 15, 18, 23, 25, 31, 38, 39, 44], "labelbottom": 45, "labelleft": 45, "laplacian": 44, "larg": [14, 38, 39], "larger": 45, "last": [0, 7, 17, 18, 19, 20, 38], "latest": 38, "latex": 38, "latter": 30, "lausann": 38, "layout": [0, 5, 23, 39], "least": 44, "left": [5, 18, 37, 38, 45], "legaci": [38, 44], "legal": 10, "len": 45, "length": 18, "less": [5, 23, 31, 34, 35, 36, 38, 39, 41], "lessen": 14, "let": [44, 45], "level": [5, 6, 15, 23, 38, 39, 44], "leverag": 38, "lfloor": 18, "librari": [5, 41], "licens": [5, 42], "lifespan": 38, "lifetim": 6, "lighten": 15, "like": [5, 6, 15, 36, 38, 39], "likewis": 23, "limit": [5, 10, 38, 39, 45], "line": [2, 3, 5, 14, 41, 42], "linear": [15, 44], "linewidth": 45, "link": [5, 18, 38, 44], "linux": 5, "list": [5, 7, 10, 11, 12, 14, 15, 17, 19, 23, 29, 31, 34, 35, 36, 37, 39], "listserv": 18, "liter": 38, "literatur": 44, "load": [0, 5, 6, 38, 41, 45], "load_data": 6, "loader": [0, 6, 38, 41], "loc": 45, "local": [5, 38], "local_hash_check": [0, 5], "locat": [10, 15, 37, 44, 45], "log": [0, 38, 39, 41], "log_dir": [0, 5], "log_level": [0, 5], "logger": [0, 5, 23, 41], "london": 38, "look": [5, 36], "lookup": 38, "loop": 15, "loosen": 38, "lower": [23, 45], "lowest": 45, "lp": 22, "lr_epi": 7, "lsqr": 38, "lw": 45, "m": [10, 42, 44], "m0scan": 23, "machin": 38, "macnicol": 38, "mag_fil": 12, "magazin": 10, "magic": 5, "magn": 44, "magnet": 18, "magneticfieldstrength": 18, "magnitud": [10, 12, 27, 30, 34, 37, 38, 44], "magnitude1": [23, 38], "magnitude2": [23, 38], "magnitude_wf": 34, "mai": [6, 7, 10, 12, 15, 18, 29, 30, 31, 34, 39, 41, 44], "main": [0, 1, 38, 45], "maint": 38, "maintain": 5, "mainten": 38, "major": [38, 44], "make": [14, 38, 42, 44], "makefil": 38, "manag": [5, 6], "mandatori": [9, 10, 11, 12, 13, 14, 23, 37], "mani": [23, 44], "manifest": 38, "manipul": [18, 20, 38], "manual": 23, "manuscript": 38, "map": [0, 10, 12, 14, 15, 17, 20, 23, 27, 29, 30, 34, 36, 37, 38, 41], "map_coordin": 45, "march": 41, "mark": 10, "markiewicz": 38, "marku": 38, "mask": [9, 10, 13, 14, 18, 22, 27, 29, 30, 34, 35, 36, 37, 38], "mask_anat": 36, "mass": 38, "massag": [34, 38], "master": [39, 44], "mat": 6, "match": [7, 10, 36, 37], "match_histogram": [0, 36], "materi": 45, "mathbf": [10, 15], "mathia": 38, "matplotlib": 45, "matric": [10, 15, 29, 38], "matrix": [15, 18, 38], "matt": 44, "matter": 18, "matthew": 38, "max": 45, "max_alpha": [13, 25], "max_concurr": 15, "max_tr": 14, "maximum": [13, 15, 29, 30, 31, 34, 38, 39], "maxtasksperchild": 5, "mean": [5, 10, 12, 23, 39, 44, 45], "measur": [34, 45], "mechan": 18, "med": 44, "median": 10, "medicin": 38, "mem": 39, "memori": [5, 15, 19, 38, 39], "memory_gb": [0, 5, 39], "merg": [36, 38], "meshgrid": 45, "messag": [23, 38], "meta": 18, "meta_dict": 37, "metadata": [0, 7, 11, 12, 14, 15, 18, 20, 23, 29, 34, 35, 36, 37, 38, 44], "metadataerror": [0, 7, 41], "method": [0, 6, 7, 15, 23, 34, 35, 36, 38, 41], "metric": 36, "mgr": 5, "mhz": 18, "middl": [25, 45], "miga": 21, "migrat": 38, "mika\u00ebl": 38, "min": 45, "miniconda": 38, "minim": [5, 38, 39, 41], "minimum": [10, 38], "minor": 38, "mirror": 15, "misc": [0, 16], "miscellan": 19, "misconfigur": 38, "miss": [23, 38], "mixin": 13, "mktemp": 5, "mm": [12, 36], "mni": 36, "mni152nlin2009casym": [5, 38, 45], "mnt": 38, "mock": 38, "mode": [5, 10, 15, 29, 30, 34, 35, 36, 38, 39, 44], "model": [14, 44, 45], "modifi": [10, 25, 38], "modul": [0, 1, 6, 8, 16, 24, 26, 28, 32, 38, 41], "moduletyp": 6, "monitor": 5, "more": [10, 12, 23, 34, 36, 37, 38, 44], "morpholog": [18, 22], "mosaic": 13, "most": [5, 7, 15, 17, 18, 20, 22, 38, 44], "motion": [10, 15, 29], "move": [10, 13, 15, 30, 38], "moving_label": 13, "mp2rage": 45, "mpl": 45, "mpl_toolkit": 45, "mprage": [10, 45], "mr": [41, 44], "mri": [34, 39, 41, 44], "mri_robust_regist": 12, "mrm": 44, "much": 45, "multi": [15, 23, 33, 38, 39, 44], "multipl": [6, 35, 38, 39, 44], "multiplex": 38, "multiproc": 5, "multiprocess": 5, "multithread": 5, "multivers": 38, "must": [5, 15, 23, 35, 42], "mutual": [10, 14, 44], "n": [6, 14, 15, 38, 39, 44], "n4": [27, 34, 38], "n_": 18, "n_proc": 38, "name": [5, 6, 7, 13, 18, 23, 27, 29, 30, 31, 34, 35, 36, 37, 38, 41], "namespac": 3, "nan": [38, 45], "natur": 22, "naveau": 38, "nb": 45, "nbm453": 44, "ndarrai": 15, "ndi": 45, "ndimag": 45, "nearest": 15, "necessari": [6, 14, 18, 23, 34, 38, 44], "need": [5, 34, 38, 45], "neg": 15, "neighbor": 44, "neither": 18, "neurodock": 42, "neuroimag": [38, 41, 42, 44], "neuroinform": 44, "neurostar": 18, "new": [5, 10, 17, 22, 41], "newest": 38, "newli": 38, "newpath": 20, "next": 38, "nibabel": [15, 22, 45], "nibabi": 38, "nice": 38, "niflow": 38, "nifti": [10, 14, 15, 23, 37, 44], "nifti1imag": [10, 15], "nii": [6, 7, 12, 18, 34, 45], "nimg": 44, "niprep": [38, 39, 41], "nipyp": [0, 4, 5, 9, 10, 12, 13, 14, 37, 38, 39, 41, 42], "nipype1": 38, "nipype_vers": [0, 5], "nitranform": 38, "niworkflow": 38, "nmr": 44, "node": 38, "nois": [10, 14, 34], "noise_imag": 14, "noise_model": 14, "noisi": 38, "nomin": [38, 45], "non": [38, 44], "nonbrain": 27, "none": [2, 3, 5, 7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 22, 23, 25, 29, 36, 37, 39, 44, 45], "nonlinear": 44, "nonneg": 15, "nonstandard": 18, "nonsteadi": 36, "nonuniform": 34, "nonzero": 44, "norm": 45, "normal": [38, 44, 45], "note": 18, "notebook": [38, 45], "noth": 7, "notic": 38, "notrack": [0, 5, 39], "novemb": 41, "now": [19, 38], "np": 45, "nproc": [0, 5, 39], "nthread": 39, "num_thread": [10, 14, 15], "number": [5, 10, 14, 15, 18, 22, 29, 30, 31, 34, 35, 36, 38, 39, 44, 45], "numpi": [15, 37, 38, 45], "nutshel": [40, 41, 44], "o": [5, 14, 15, 34, 37, 38, 44], "obj": [15, 34], "object": [5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 23, 37, 38, 45], "obliqu": [10, 14, 22, 38, 44], "obtain": [10, 18, 22, 39, 44], "occurr": 39, "octob": 41, "odd": [10, 38], "oe": 18, "oesteban": 5, "off": 38, "offer": 41, "offset": 44, "old": 38, "omp": 39, "omp_nthread": [0, 5, 29, 30, 31, 34, 35, 36, 39], "onc": 18, "one": [10, 12, 15, 22, 23, 34, 38, 44], "ones_lik": 45, "onli": [5, 14, 15, 22, 23, 38, 39, 44, 45], "onto": [10, 15, 44], "opaque_perc": 25, "open": [39, 41], "openneuro": 23, "openpgp": 38, "oper": [5, 6, 15, 18, 22, 38, 39], "oppos": [35, 45], "opt": [5, 39], "optim": [10, 38, 44], "option": [5, 9, 10, 11, 12, 13, 14, 15, 18, 23, 27, 31, 35, 36, 37, 38, 41, 44], "oracl": 38, "orchestr": 38, "order": [15, 22, 25, 38], "org": 38, "orient": [10, 22, 38, 45], "origin": [5, 10, 14, 15, 37, 38, 45], "ornt_transform": 22, "orthogon": 35, "oscar": 38, "osf": 38, "oslo": 38, "other": [0, 10, 15, 22, 23, 38, 41, 42], "other_packag": 6, "otherwis": [19, 38], "our": [15, 23, 38, 45], "out": [5, 15, 37, 38, 39], "out_": 31, "out_brain": 27, "out_coeff": 10, "out_correct": 10, "out_data": [11, 14], "out_epi": 14, "out_error": 10, "out_extrapol": 10, "out_field": [10, 14], "out_fil": [9, 12, 14, 18, 22, 27, 37], "out_intercept": 10, "out_list": 14, "out_mask": [9, 14, 27], "out_meta": [14, 37], "out_path_bas": 37, "out_probseg": [9, 27], "out_report": 13, "out_warp": [36, 38], "outcom": 44, "outlier": 38, "output": [0, 5, 9, 10, 11, 12, 13, 14, 15, 26, 27, 29, 30, 31, 34, 35, 36, 38, 39, 44], "output_dir": [0, 5, 31, 37, 39], "output_dtyp": 15, "output_imag": 14, "outputnod": 38, "outsid": [10, 13, 15, 38], "over": [6, 15, 18, 38], "overcommit": 5, "overcommit_limit": [0, 5], "overcommit_polici": [0, 5], "overestim": 38, "overflow": 15, "overhaul": 38, "overlai": 25, "overlay_param": 25, "overli": 38, "overload": 37, "overrid": [15, 38], "overwrit": 7, "p": [5, 10, 44], "pa": [23, 38], "pacifi": 38, "packag": [0, 38, 41, 42], "pad": [14, 22, 38], "padslic": [0, 14], "page": 38, "pair": [12, 17, 23, 34, 38], "pandoc": 38, "parallel": [5, 15, 18, 35, 36, 39, 44], "parallelreductionfactorinplan": 18, "param": 45, "paramet": [5, 7, 12, 14, 15, 18, 22, 23, 27, 29, 30, 31, 34, 35, 36, 37, 38, 44], "parekh": 18, "pars": 3, "parse_arg": [0, 3], "parser": [0, 1], "part": [34, 38, 41], "partial": 38, "particip": [5, 23, 31, 39], "participant_id": 5, "participant_label": [0, 5, 39], "particular": [5, 17, 34, 45], "particularli": 38, "pass": [5, 6, 12, 22, 23, 38, 44], "patch": [10, 38], "path": [0, 5, 6, 7, 10, 15, 19, 34, 35, 36, 37, 38, 39, 42], "pathlik": [9, 10, 11, 12, 13, 14, 15, 34, 37], "pdb": [0, 5, 39], "pdf": [29, 30, 34, 35, 36], "pe": [11, 18, 29, 35, 36, 44], "pe_dir": [10, 11, 12, 14, 15, 22], "pe_dir_fsl": 11, "pe_direct": 11, "pe_dirs_fsl": 11, "pe_info": 15, "pennsylvania": 38, "pep517": 38, "pepolar": [0, 10, 23, 30, 32, 38, 41], "pepolar4p": 23, "pepolar_estimate_wf": 35, "per": [15, 18, 23, 34, 38], "perelman": 38, "perfect": 10, "perform": [7, 22, 30, 38, 41, 44], "permiss": 38, "perturb": 45, "phase": [10, 12, 15, 20, 23, 34, 35, 36, 38, 41, 45], "phase1": [12, 34, 38], "phase2": [12, 34], "phase_diff": 12, "phasediff": [10, 12, 23, 34, 38, 44], "phasediff2fieldmap": [0, 12], "phaseencodingdirect": [15, 18, 22, 23], "phasemanip": [0, 16], "phasemap2rad": [0, 12], "phdiff2fmap": [0, 20], "phdiff_wf": 34, "phenomenon": [40, 41], "philip": 18, "phyisic": 45, "physic": [15, 40, 41, 44], "pi": [34, 44], "pick": [14, 23], "pickl": 5, "pictur": 45, "piec": 38, "piecewis": 15, "pin": 38, "ping": 21, "pinsard": 38, "pip": 42, "pipelin": [38, 44], "pixel": [10, 18], "pkg_resourc": 38, "pkgdata": 6, "place": 23, "plan": 5, "planar": [41, 44, 45], "plane": 18, "platform": [5, 41], "plausibli": 44, "pleas": [18, 38], "plo": 44, "plot": [25, 38, 45], "plot_brain": 45, "plot_param": 25, "plot_registr": [0, 25], "plt": 45, "plugin": [0, 5, 39], "plugin_arg": [0, 5], "plumb": [10, 14, 38], "png": [29, 30, 34, 35, 36], "point": [2, 10, 15, 38, 44], "polar": [14, 22, 38, 44], "poldrack": 38, "polici": 5, "pone": 44, "pop": 19, "popul": 38, "posit": [10, 14, 22, 41, 44], "positivedirectioncosin": [0, 14], "posix": 5, "posixpath": 5, "possibl": [5, 6, 18, 23, 39, 44], "post": 18, "posterior": 36, "postprocess": 38, "potenti": [14, 38], "ppm": 18, "pr": 38, "pravesh": 18, "pre": [41, 44], "precis": [5, 31], "precomput": 22, "precondit": 10, "prefer": 18, "prefilt": [15, 22], "prefix": [5, 39], "prelud": 34, "prepar": [21, 34, 36, 38, 44], "prepopul": 39, "preprocess": [5, 18, 31, 34, 36, 37, 38, 41, 44], "present": [23, 38], "prevent": 38, "previou": [15, 38, 44], "previous": [5, 38, 39], "principl": 10, "print": 42, "prior": 38, "priorit": 38, "prioriti": 23, "probabilist": 9, "probabl": 27, "probe": 19, "problem": [10, 18, 38, 44, 45], "procedur": 44, "process": [5, 10, 22, 29, 30, 31, 34, 39, 41, 44], "processor": 39, "produc": [30, 38, 44, 45], "product": [10, 15, 22, 38, 45], "program": [6, 14, 38, 39, 41], "progress": 10, "project": [10, 22, 44], "promin": [38, 44], "propag": [15, 37], "properti": [17, 22], "proport": 44, "propos": 44, "protocol": [38, 41, 44], "proton": 44, "provid": [6, 7, 15, 18, 23, 34, 38, 39, 41, 44], "psi": [10, 15], "psl": 22, "psychologi": 38, "pull": 38, "purpos": [23, 30, 44], "push": 38, "put": 38, "pybid": [5, 23, 38, 39], "pypi": 42, "pyplot": 45, "python": [5, 6, 21, 38, 39, 41, 42], "q": [10, 45], "qualifi": 6, "qualiti": 30, "qualnam": 7, "quantit": 44, "queri": [23, 38], "quick": [18, 22], "quit": 18, "quiver": 45, "r": [38, 44, 45], "ra": [10, 15, 22, 38], "rad": [7, 12, 20, 38], "radian": [12, 44], "radiologi": 38, "radiu": [9, 12], "rais": 18, "raise_insuffici": 5, "ram": 5, "random": [27, 38], "rang": [12, 15, 34, 38, 44], "rather": [10, 15, 38, 44], "ratio": [18, 44], "rcparam": 45, "rdpu_r": 45, "re": [5, 38, 39], "reach": 27, "read": [5, 6, 7, 20], "read_text": 6, "readabl": [0, 6, 41], "readout": [10, 11, 12, 15, 18, 29, 44], "readout_tim": 11, "real": 39, "realign": 15, "realiti": 45, "realli": 38, "reason": [10, 38], "reced": 10, "receiv": [7, 44], "recent": [7, 10, 17, 18, 20, 34], "reconstruct": [10, 15, 18, 44], "reddish": 45, "reduc": 45, "ref_mask": 36, "refacor": 38, "refactor": 38, "refer": [10, 13, 14, 15, 22, 23, 27, 29, 30, 31, 34, 35, 36, 37, 38, 41, 45], "reference_label": 13, "reflect": 15, "refresh": 38, "regard": [5, 18], "region": [34, 36, 44, 45], "regist": [12, 15, 38], "registr": [0, 12, 13, 15, 28, 36, 38, 39, 41], "registri": [7, 23, 38], "regress": 12, "regular": [10, 15, 36, 45], "rel": [6, 38, 42], "relai": 23, "relat": [38, 41], "relax": 38, "releas": 41, "relev": 38, "reli": 34, "reliabl": 38, "remain": 6, "remot": 38, "remov": [5, 10, 15, 27, 34, 38, 39], "remove_node_directori": [0, 5], "renam": 38, "render": 38, "reobliqu": [0, 14], "reorient": [14, 22, 38], "reorient_pedir": [0, 22], "reorientimageandmetadata": [0, 14], "repeat": 17, "replac": [7, 27, 38], "repo": 38, "report": [5, 13, 18, 37, 38], "reportcapableinterfac": 13, "reportlet": [0, 8, 38], "repres": [5, 7, 9, 10, 11, 12, 13, 14, 15, 37, 44], "represent": [5, 15, 38, 44], "reproduc": 41, "request": [6, 22, 38], "requir": [6, 21, 34, 38, 41, 42], "rerun": 38, "resampl": [10, 14, 15, 22, 30, 36, 38], "resample_to_zoom": [0, 22], "research": 44, "reshap": 45, "resolut": [22, 38, 45], "resolv": [10, 38], "reson": 44, "resort": 44, "resourc": [5, 6, 38], "resource_monitor": [0, 5, 9, 10, 11, 12, 14], "respect": 22, "respons": [0, 41], "restor": 5, "restore_env": [0, 5, 41], "restrict": [36, 38], "result": [5, 6, 10, 15, 38, 39, 44, 45], "retain": 10, "retouch": 38, "return": [7, 15, 17, 19, 22, 23, 38, 45], "retval": [4, 5], "reus": [15, 38], "revers": [15, 17, 18, 44], "review": 18, "revis": [10, 38], "rf": 38, "rfloor": 18, "rician": 14, "ridge_alpha": 10, "right": [18, 19, 37], "rigid": 10, "ro": [18, 44], "ro_tim": [10, 12, 15], "robust": [38, 41, 44], "robustaverag": 38, "rodent": 38, "roll": 38, "root": [5, 7, 10, 38, 39], "rootlogg": 5, "rorden": 18, "ross": 38, "rot_thresh": 12, "rotat": [10, 12, 22, 38, 44], "rotim": 18, "round": 45, "run": [3, 5, 12, 14, 23, 29, 30, 34, 35, 36, 38, 39], "run_unique_id": 5, "run_uuid": [0, 5], "runner": [5, 38, 39], "runtim": 5, "russel": 38, "s1053": 44, "s_": [44, 45], "s_1": 15, "s_2": 15, "s_3": 15, "sagitt": 25, "same": [6, 10, 12, 14, 15, 38, 39, 44], "sampl": [10, 15, 22], "sampled_field": 45, "samples_i": 45, "samples_x": 45, "sanit": [7, 38], "sanitized_id": [0, 7, 38], "sar": 10, "satterthwait": 38, "save": [14, 31, 37, 38], "save_nois": 14, "sbref": [23, 38], "scalar": 14, "scale": [25, 29, 34, 38, 45], "scale_unit": 45, "scan": [15, 18, 41, 44, 45], "scanner": [38, 44, 45], "scatter": 45, "scheme": [41, 44, 45], "school": 38, "scipi": [38, 45], "scm": 38, "scope": 6, "scrutin": 44, "sd": [36, 44, 45], "sd_prior": 36, "sd_syn": 6, "sd_syn_sloppi": 6, "sdc": [10, 15, 23, 27, 31, 38, 44], "sdcflow": [0, 39, 42, 44, 45], "search": [7, 23, 44], "second": [10, 15, 18, 36, 44], "secret": 38, "section": [0, 15, 41, 44], "see": [5, 15, 23, 38, 44, 45], "seed": 38, "seem": 18, "seen": 45, "segfault": [10, 14], "segment": [6, 44], "sei": [38, 44], "seismic": 45, "select": [38, 45], "self": [17, 38], "semaphor": 15, "send": [21, 39], "send_crumb": [0, 21], "sens": 18, "sensit": 38, "separ": [6, 27, 34, 38], "septemb": 41, "sequenc": [15, 34, 41], "seri": [15, 41], "serv": 37, "server": 21, "session": [5, 23, 38, 39, 44], "session_label": [0, 5, 39], "set": [5, 10, 15, 18, 23, 29, 36, 37, 38, 39, 42, 44], "set_aspect": 45, "set_input": 7, "set_ticklabel": 45, "set_xlim": 45, "set_xticklabel": 45, "set_ylim": 45, "set_yticklabel": 45, "setup": [21, 38], "setup_miga": [0, 21], "setuptool": 38, "setuptools_scm": 38, "sever": [38, 39, 44], "sha256": 5, "shape": [10, 12, 15, 38, 45], "share": [5, 38, 39], "shift": [12, 15, 18, 44], "shim": [38, 44], "short": [34, 35, 36], "shortest": 38, "should": [5, 7, 12, 13, 14, 15, 18, 22, 23, 34, 35, 36, 37, 38, 39, 44, 45], "show": [13, 38, 39], "shown": 13, "shrink": 14, "shrink_factor": 14, "sici": 44, "sidecar": [7, 18], "siemens2rad": 38, "sign": 15, "signal": [10, 38, 45], "significantli": 12, "similar": 38, "similarli": 23, "simpl": 38, "simplebeforeaft": 38, "simpleinterfac": [9, 10, 11, 12, 14], "simpli": 6, "simplic": 44, "simplifi": [23, 38], "simplist": 38, "simultan": 39, "singl": [5, 14, 15, 23, 31, 38, 39, 44], "singleton": 5, "sitek": 38, "size": [18, 29], "sjshim": 38, "sk": 38, "skim": 38, "skip": 23, "skull": [30, 34, 36, 44], "slice": [14, 38, 44, 45], "slightli": [15, 45], "sloppi": [0, 5, 29, 30, 31, 34, 35, 36, 38, 39], "small": 38, "smaller": 38, "smart": 27, "smeisler": 38, "smooth": [10, 44], "smriprep": 38, "sneve": 38, "so": [6, 10, 11, 12, 36, 38, 44, 45], "soft": 27, "softwar": [38, 42, 44], "solver": 38, "some": [5, 6, 7, 18, 23, 27, 34, 38, 42, 44, 45], "somewher": 19, "sort": [7, 11, 27, 38], "sortpeblip": [0, 11], "sourc": [0, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 25, 27, 29, 30, 31, 33, 34, 35, 36, 37, 41, 44], "source_fil": 37, "source_ornt": 22, "space": [10, 15, 18, 29, 30, 36, 37, 38, 39, 44, 45], "spars": 15, "spatial": [10, 14, 15], "spatialimag": [15, 22, 38], "speci": [0, 5], "special": [7, 13, 17, 38], "specif": [0, 7, 38, 41, 45], "specifi": [14, 36, 38], "speech": 38, "spgr": 45, "sphinx": 38, "spike": 10, "spin": 44, "spinoza": 18, "spiral": 38, "spline": [10, 15, 27, 29, 34, 35, 36, 38, 44], "split": 38, "spread": 44, "sqlite": 5, "squeez": 38, "sra": 10, "stabil": 38, "stabl": 38, "stack": 14, "stage": [10, 44], "standalon": [2, 3, 4, 38, 41], "standard": [14, 18, 38, 39], "stanford": 38, "start": [5, 7, 38, 45], "stat": 38, "state": [36, 41], "statement": 18, "std2anat_xfm": 36, "step": [10, 15, 44, 45], "stop": [5, 38], "stop_on_first_crash": [0, 5], "store": [5, 18, 37, 39, 44], "str": [5, 6, 7, 14, 15, 23, 27, 29, 30, 31, 34, 35, 36, 37], "strang": 18, "strategi": [7, 10, 15, 31, 38, 44], "strength": [18, 45], "string": [5, 9, 10, 11, 12, 13, 14, 23, 37], "strip": [30, 34, 36, 44], "strong": 36, "structur": [5, 9, 15, 23, 38, 44], "studholm": 44, "studholme2000": 44, "studi": 44, "style": 30, "sub": [5, 7, 39, 45], "subject": [5, 23, 31, 33, 38], "submit": [12, 38], "submodul": [0, 38, 41, 44], "suboptim": 5, "subordin": 38, "subpackag": [0, 41], "subplot": 45, "subprocess": 5, "subsequ": [34, 44], "subtract": [34, 38], "subtract_phas": [0, 20], "subtractphas": [0, 12], "successfulli": 23, "suffer": 44, "suffici": [38, 45], "suffix": [0, 5, 7, 23, 38, 39, 45], "suit": [38, 44], "sum_": 15, "summar": 18, "summari": 44, "sunja": 38, "support": [4, 15, 34, 35, 36, 38], "sure": [38, 42], "surfac": 44, "surround": 34, "suscept": [15, 23, 36, 38, 40, 41, 44], "svg": [13, 29, 30, 34, 35, 36], "svgutil": 38, "swapax": 45, "switch": [5, 38], "symmetr": 44, "symmetri": 44, "syn": [0, 10, 14, 32, 38, 44], "syn_preprocessing_wf": 36, "syn_sdc_wf": 36, "system": [14, 22, 39, 42], "t": [10, 15, 18, 20, 44, 45], "t1": 41, "t1w": [7, 23, 36, 38, 44, 45], "t1w_invers": 36, "t2": [36, 45], "t2w": [36, 38, 44], "t_": [18, 44], "t_mask": 36, "tabl": [7, 38], "tag": [15, 18, 38, 44], "take": [34, 35, 44], "taken": 35, "target": [5, 10, 15, 22, 29, 30, 37, 38, 44], "target2fmap_xfm": [30, 38], "target_affin": 15, "target_mask": 30, "target_nii": 15, "target_orient": 14, "target_ornt": 22, "target_ref": 30, "target_refer": 15, "task": [5, 35, 36], "te": [20, 34, 44], "techniqu": 41, "technologi": 38, "telemetri": [0, 16], "templat": [5, 36], "template_id": [0, 5], "templateflow": [5, 45], "templateflow_hom": [0, 5], "templateflow_vers": [0, 5], "temporari": [6, 15], "tensor": [10, 15, 38, 44], "tesla": 44, "test": [5, 23, 38], "test_wrangler_uri": 38, "texliv": 38, "text": [5, 18, 20, 34, 44], "than": [10, 38], "thank": 38, "thei": [11, 38, 44], "them": 12, "themselv": 38, "theodor": 38, "theoret": 38, "theori": 41, "therefor": [10, 15, 22, 35, 44], "thereof": 30, "thesi": 44, "theta": 44, "theta_i": 44, "thi": [5, 6, 7, 10, 12, 14, 15, 18, 21, 22, 23, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 44], "think": 45, "third": 17, "thorough": 18, "those": [10, 44, 45], "thread": [5, 10, 14, 29, 30, 31, 34, 38, 39], "three": 44, "threshold": [12, 36], "through": [6, 10, 12, 14, 15, 38], "throughout": 6, "thu": 22, "tick": 45, "time": [5, 6, 10, 11, 12, 14, 15, 18, 29, 38, 39, 44], "timepoint": [10, 36], "tissu": [27, 45], "tmp": 5, "to_displac": [0, 15], "to_filenam": [0, 5, 41], "togeth": [36, 38], "toler": [22, 38], "toml": 5, "tool": [0, 5, 15, 16, 25, 38, 41, 42, 45], "top": [6, 39, 45], "topup": [10, 11, 14, 35, 38, 44], "topupcoeffreori": [0, 10], "total": [5, 11, 12, 15, 18, 44], "total_memori": [0, 5], "totalreadouttim": [7, 18], "toward": [38, 45], "tr": 14, "trace": 30, "traceback": [7, 17, 18, 20], "track": [5, 17, 39], "train": 18, "tran": 44, "trans_thresh": 12, "transax": 45, "transform": [0, 10, 12, 22, 30, 36, 41, 44], "transformcoeffici": [0, 10], "transit": 38, "translat": 12, "translation_rigid": 6, "transpar": [25, 38], "transparent_perc": 25, "travers": 6, "travisci": 38, "treat": [6, 14], "treatment": 38, "treiber": 44, "treiber2016": 44, "tri": 14, "trigger": [38, 39], "trivial": 10, "trt": 45, "true": [5, 6, 7, 10, 12, 14, 15, 17, 21, 22, 23, 29, 36, 37, 39, 44, 45], "truth": 45, "try": 44, "tune": 38, "tupl": [7, 10, 14, 15, 19, 34, 36, 45], "turn": 45, "two": [12, 18, 20, 22, 23, 34, 35, 38, 39, 44, 45], "txt": [5, 17], "type": [7, 11, 12, 15, 17, 23, 37, 44], "typeerror": 17, "typic": [6, 15, 41, 44], "typo": 38, "u": [12, 20, 45], "ubuntu": 38, "ucbn": 38, "um": 38, "un": 38, "unavil": 38, "uncompress": 37, "under": [5, 38, 39], "underscor": 7, "understand": 45, "undistort": 10, "uneven": 14, "unhash": 17, "uniform": [38, 44], "uniformgrid": [0, 14], "union": [0, 9], "uniqu": [5, 7, 29, 30, 34], "unit": [7, 12, 15, 20, 29, 34, 37, 38], "unittest": 38, "univers": 38, "universit\u00e4t": 44, "unknown": [5, 39], "unless": [15, 38], "unmodifi": 37, "unpack": 6, "unsaf": 38, "unsanit": 38, "unser": 10, "unser1999": [10, 15], "unsupport": 41, "untouch": 19, "unus": 38, "unwarp": [10, 15, 29, 35, 36, 38, 41], "unwarp_parallel": [0, 15, 41], "unwarp_wf": [29, 38], "unwrap": [34, 38, 44], "up": [5, 6, 29, 36, 37, 38, 42, 44], "updat": [10, 12, 15, 22, 38, 44], "upgrad": 38, "upload": 38, "upper": [15, 39], "upstream": 38, "uri": 38, "url": 38, "us": [5, 6, 7, 10, 12, 14, 15, 18, 22, 23, 29, 30, 31, 34, 36, 38, 39, 42, 44], "usa": 38, "usabl": 38, "usag": [0, 6, 41], "use_plugin": 39, "user": [5, 23, 34, 38, 41], "util": [0, 5, 7, 8, 15, 24, 38, 41, 44], "ux": 38, "v": [14, 39, 44, 45], "v1": 38, "val": 17, "valid": [7, 15, 18, 23, 38, 39], "valu": [5, 7, 9, 10, 11, 12, 13, 14, 15, 17, 23, 37, 38, 45], "valueerror": [7, 17, 18, 20, 38], "variabl": [5, 14], "variat": 44, "variou": [11, 12], "vector": 45, "vein": 38, "veloc": 44, "vendor": 18, "ventricl": 45, "verbos": [5, 14, 38, 39], "veri": [23, 45], "verifi": 12, "version": [0, 5, 7, 14, 38, 39, 42], "via": [5, 44], "view": [25, 38, 45], "virtual": 5, "vision": 38, "visual": [13, 25, 38, 44, 45], "viz": [0, 41], "vmax": 45, "vmin": 45, "volum": [15, 35, 36, 38, 45], "voxel": [10, 15, 22, 27, 29, 36, 44, 45], "voxel_centers_c": 45, "voyag": 18, "vsm": [15, 38, 44], "vvv": 39, "w": [18, 38, 39], "wa": [14, 15, 34, 35, 36, 37, 38], "wai": 38, "walker": 27, "wang": 44, "wang2017": 44, "want": [7, 15, 39, 44], "warn": [5, 38], "warp": [14, 36, 44, 45], "warped_brain": 45, "warped_edg": 45, "water": 18, "waterfatshift": 18, "we": [7, 10, 12, 15, 23, 34, 38, 44, 45], "weekli": 38, "weight": [15, 38, 41], "well": [10, 38, 44], "were": [38, 44], "wf": 18, "what": [39, 41], "when": [5, 6, 7, 10, 15, 23, 34, 38, 39, 44, 45], "whenev": [5, 38], "where": [5, 6, 10, 12, 13, 15, 18, 36, 39, 44, 45], "whether": [5, 12, 22, 29, 34, 35, 36, 37, 45], "which": [5, 7, 10, 11, 12, 14, 15, 18, 31, 35, 37, 38, 39, 44, 45], "while": 38, "white": 45, "whole": 4, "whose": [5, 22], "why": 10, "wide": [5, 33], "width": 45, "wipe": [5, 39], "wire": 38, "within": [10, 18, 38, 39, 44, 45], "without": [10, 12, 14, 36, 38], "wm": 38, "wonder": 18, "word": [10, 15, 22], "work": [5, 38, 39, 45], "work_dir": [0, 5, 39], "workabl": 44, "workdir": 38, "worker": [0, 15, 41], "workflow": [0, 1, 5, 7, 23, 38, 41, 44], "world": 39, "would": [6, 45], "wrangler": [0, 16, 38, 44], "wrap": [6, 12, 14, 15, 34, 44], "write": [5, 37, 38], "write_coeff": [30, 37], "write_graph": [0, 5], "written": [5, 37, 42], "wrong": [18, 38], "x": [10, 11, 14, 25, 41], "x1": 45, "x2": 45, "x_coord": 45, "xfm": [15, 22], "xfm_data2fmap": 15, "xtick": 45, "xxxxx": 39, "xy": 45, "xyz_nii": 15, "y": [10, 11, 14, 25, 38], "y1": 45, "y2": 45, "y_coord": 45, "y_coord_mov": 45, "yield": [6, 44], "you": 39, "your": [15, 42, 45], "ytick": 45, "z": [10, 11, 14, 25, 38], "z_": 45, "z_slice": 45, "zaitsev": 44, "zaitsev2004": 44, "zero": [10, 13, 23, 38, 45], "zip": [6, 45], "zoom": [10, 22, 38, 44], "zooms_min": 10}, "titles": ["Library API (application program interface)", "sdcflows.cli package", "sdcflows.cli.main module", "sdcflows.cli.parser module", "sdcflows.cli.workflow module", "sdcflows.config module", "sdcflows.data package", "sdcflows.fieldmaps module", "sdcflows.interfaces package", "sdcflows.interfaces.brainmask module", "sdcflows.interfaces.bspline module", "sdcflows.interfaces.epi module", "sdcflows.interfaces.fmap module", "sdcflows.interfaces.reportlets module", "sdcflows.interfaces.utils module", "sdcflows.transform module", "sdcflows.utils package", "sdcflows.utils.bimap module", "sdcflows.utils.epimanip module", "sdcflows.utils.misc module", "sdcflows.utils.phasemanip module", "sdcflows.utils.telemetry module", "sdcflows.utils.tools module", "sdcflows.utils.wrangler module", "sdcflows.viz package", "sdcflows.viz.utils module", "sdcflows.workflows package", "sdcflows.workflows.ancillary module", "sdcflows.workflows.apply package", "sdcflows.workflows.apply.correction module", "sdcflows.workflows.apply.registration module", "sdcflows.workflows.base module", "sdcflows.workflows.fit package", "sdcflows.workflows.fit.base module", "sdcflows.workflows.fit.fieldmap module", "sdcflows.workflows.fit.pepolar module", "sdcflows.workflows.fit.syn module", "sdcflows.workflows.outputs module", "What\u2019s new?", "Standalone command line usage", "Examples", "SDCFlows", "Installation", "&lt;no title&gt;", "Methods and implementation", "Susceptibility Distortions in a nutshell"], "titleterms": {"": 38, "0": [38, 45], "01": 38, "04": 38, "05": 38, "07": 38, "08": 38, "09": 38, "1": 38, "10": 38, "11": 38, "12": 38, "13": 38, "14": 38, "15": 38, "16": 38, "18": 38, "2": 38, "20": 38, "2019": 38, "2020": 38, "2021": 38, "2022": 38, "2023": 38, "2024": 38, "22": 38, "23": 38, "24": 38, "25": 38, "26": 38, "27": 38, "29": 38, "3": 38, "30": 38, "4": 38, "5": 38, "6": 38, "7": 38, "8": 38, "9": 38, "The": 45, "absolut": 45, "acquisit": 45, "also": 18, "ancillari": 27, "api": 0, "appli": [28, 29, 30], "applic": 0, "approach": 44, "april": 38, "argument": 39, "august": 38, "author": 38, "b0": 44, "b0fieldidentifi": 44, "b_": 45, "base": [31, 33, 38], "bid": [39, 44], "bimap": 17, "blip": 45, "brain": 45, "brainmask": 9, "bspline": 10, "chang": 38, "cli": [1, 2, 3, 4], "cocktail": 45, "command": 39, "config": 5, "configur": 5, "content": [40, 41], "correct": 29, "data": [6, 44, 45], "dataset": 44, "decemb": 38, "depend": 42, "differ": 44, "direct": [44, 45], "discov": 44, "distort": [44, 45], "effect": 45, "epi": 11, "epimanip": 18, "estim": 44, "exampl": 40, "explicit": 44, "extern": 42, "februari": 38, "field": 45, "fieldmap": [7, 34, 44], "fit": [32, 33, 34, 35, 36], "fmap": 12, "handl": 39, "i": 45, "imag": 44, "implement": 44, "implicit": 44, "ingredi": 45, "instal": 42, "instrument": 39, "intendedfor": 44, "interfac": [0, 8, 9, 10, 11, 12, 13, 14], "januari": 38, "juli": 38, "june": 38, "less": 44, "librari": 0, "line": 39, "list": 38, "log": 5, "mai": 38, "main": 2, "map": 44, "march": 38, "method": 44, "misc": 19, "modul": [2, 3, 4, 5, 7, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 25, 27, 29, 30, 31, 33, 34, 35, 36, 37], "mri": 45, "name": 39, "neg": 45, "new": 38, "novemb": 38, "nutshel": 45, "octob": 38, "off": 45, "option": 39, "other": [5, 44], "output": 37, "packag": [1, 6, 8, 16, 24, 26, 28, 32], "paper": 38, "parser": 3, "pe": 45, "pepolar": [35, 44], "perform": 39, "phase": 44, "phasemanip": 20, "phenomenon": 45, "physic": 45, "posit": 39, "pre": 38, "program": 0, "refer": 44, "registr": [30, 44], "relat": 39, "releas": 38, "reportlet": 13, "respons": 5, "revers": 45, "sampl": 45, "sdcflow": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41], "second": 45, "section": 5, "see": 18, "septemb": 38, "sequenc": 44, "seri": 38, "specif": 44, "standalon": 39, "submodul": [1, 8, 16, 24, 26, 28, 32], "subpackag": 26, "suscept": 45, "syn": 36, "t1": 44, "techniqu": 44, "telemetri": 21, "text": 45, "thank": 18, "theori": 44, "thi": 45, "tool": [22, 44], "trade": 45, "transform": 15, "uniform": 45, "unsupport": 44, "unwarp": 44, "usag": [5, 39], "util": [14, 16, 17, 18, 19, 20, 21, 22, 23, 25], "viz": [24, 25], "weight": 44, "what": 38, "workflow": [4, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37], "wrangler": 23, "x": 38}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"0.1.0 (July 22, 2019)": [[38, "july-22-2019"]], "0.1.1 (July 23, 2019)": [[38, "july-23-2019"]], "0.1.2 (October 10, 2019)": [[38, "october-10-2019"]], "0.1.3 (October 15, 2019)": [[38, "october-15-2019"]], "0.1.4 (November 22, 2019)": [[38, "november-22-2019"]], "1.0.0 (November 25, 2019)": [[38, "november-25-2019"]], "1.0.1 (December 04, 2019)": [[38, "december-04-2019"]], "1.0.2 (December 18, 2019)": [[38, "id1"]], "1.0.3 (December 18, 2019)": [[38, "december-18-2019"]], "1.0.4 (January 27, 2020)": [[38, "january-27-2020"]], "1.0.5 (February 14, 2020)": [[38, "february-14-2020"]], "1.0.6 (April 15, 2020)": [[38, "april-15-2020"]], "1.1.0 (February 3, 2020)": [[38, "february-3-2020"]], "1.2.0 (February 15, 2020)": [[38, "february-15-2020"]], "1.2.1 (April 01, 2020)": [[38, "april-01-2020"]], "1.2.2 (April 16, 2020)": [[38, "april-16-2020"]], "1.3.0 (May 4, 2020)": [[38, "may-4-2020"]], "1.3.1 (May 22, 2020)": [[38, "may-22-2020"]], "1.3.2 (August 14, 2020)": [[38, "august-14-2020"]], "1.3.3 (September 4, 2020)": [[38, "september-4-2020"]], "1.3.4 (July 07, 2023)": [[38, "july-07-2023"]], "1.3.5 (February 14, 2024)": [[38, "february-14-2024"]], "1.3.x series": [[38, "x-series"]], "2.0.0 (January 25, 2021)": [[38, "january-25-2021"]], "2.0.1 (March 05, 2021)": [[38, "march-05-2021"]], "2.0.10 (December 13, 2021)": [[38, "december-13-2021"]], "2.0.11 (January 22, 2022)": [[38, "january-22-2022"]], "2.0.12 (February 08, 2022)": [[38, "february-08-2022"]], "2.0.13 (April 08, 2022)": [[38, "april-08-2022"]], "2.0.2 (May 11, 2021)": [[38, "may-11-2021"]], "2.0.3 (May 14, 2021)": [[38, "may-14-2021"]], "2.0.4 (May 18, 2021)": [[38, "may-18-2021"]], "2.0.5 (August 24, 2021)": [[38, "august-24-2021"]], "2.0.6 (September 1, 2021)": [[38, "september-1-2021"]], "2.0.7 (September 30, 2021)": [[38, "september-30-2021"]], "2.0.8 (October 15, 2021)": [[38, "october-15-2021"]], "2.0.9 (November 16, 2021)": [[38, "november-16-2021"]], "2.1.0 (May 26, 2022)": [[38, "may-26-2022"]], "2.1.1 (August 29, 2022)": [[38, "august-29-2022"]], "2.10.0 (July 04, 2024)": [[38, "july-04-2024"]], "2.11.0 (December 18, 2024)": [[38, "december-18-2024"]], "2.2.0 (December 09, 2022)": [[38, "december-09-2022"]], "2.2.1 (December 12, 2022)": [[38, "december-12-2022"]], "2.2.2 (January 04, 2023)": [[38, "january-04-2023"]], "2.3.0 (March 01, 2023)": [[38, "march-01-2023"]], "2.4.0 (March 10, 2023)": [[38, "march-10-2023"]], "2.4.1 (March 20, 2023)": [[38, "march-20-2023"]], "2.4.2 (April 20, 2023)": [[38, "april-20-2023"]], "2.4.3 (April 24, 2023)": [[38, "april-24-2023"]], "2.5.0 (June 01, 2023)": [[38, "june-01-2023"]], "2.5.1 (June 08, 2023)": [[38, "june-08-2023"]], "2.5.2 (November 09, 2023)": [[38, "november-09-2023"]], "2.6.0 (November 10, 2023)": [[38, "november-10-2023"]], "2.7.0 (December 18, 2023)": [[38, "december-18-2023"]], "2.8.0 (January 10, 2024)": [[38, "january-10-2024"]], "2.8.1 (January 22, 2024)": [[38, "january-22-2024"]], "2.9.0 (June 13, 2024)": [[38, "june-13-2024"]], "Author list for papers based on SDCFlows 2.0.x series": [[38, null]], "BIDS Specification": [[44, null], [44, null], [44, null], [44, null], [44, null], [44, null]], "CHANGES": [[38, "changes"]], "Configuration sections": [[5, "configuration-sections"]], "Contents": [[41, "contents"]], "Contents:": [[40, null]], "Data: a brain": [[45, "Data:-a-brain"]], "Direct B0 mapping sequences": [[44, "direct-b0-mapping-sequences"]], "Discovering fieldmaps in a BIDS dataset": [[44, "discovering-fieldmaps-in-a-bids-dataset"]], "Estimation tooling": [[44, "estimation-tooling"]], "Examples": [[40, null]], "Explicit specification with B0FieldIdentifier": [[44, "explicit-specification-with-b0fieldidentifier"]], "External Dependencies": [[42, "external-dependencies"]], "Fieldmap estimation: theory and methods": [[44, "fieldmap-estimation-theory-and-methods"]], "Fieldmap-less approaches": [[44, "fieldmap-less-approaches"]], "Fieldmap-less by registration to a T1-weighted image": [[44, "fieldmap-less-by-registration-to-a-t1-weighted-image"]], "Implicit specification with IntendedFor": [[44, "implicit-specification-with-intendedfor"]], "Installation": [[42, null]], "Instrumental options": [[39, "sdcflows.cli.parser-_parser-instrumental-options"]], "Library API (application program interface)": [[0, null]], "Logging": [[5, "logging"]], "Methods and implementation": [[44, null]], "Named Arguments": [[39, "sdcflows.cli.parser-_parser-named-arguments"]], "Options related to BIDS": [[39, "sdcflows.cli.parser-_parser-options-related-to-bids"]], "Options to handle performance": [[39, "sdcflows.cli.parser-_parser-options-to-handle-performance"]], "Other (unsupported) approaches": [[44, "other-unsupported-approaches"]], "Other responsibilities": [[5, "other-responsibilities"]], "PEPOLAR techniques": [[44, "pepolar-techniques"]], "Phase-difference B0 estimation": [[44, "phase-difference-b0-estimation"]], "Positional Arguments": [[39, "sdcflows.cli.parser-_parser-positional-arguments"]], "Pre-1.3.x releases": [[38, "pre-1-3-x-releases"]], "References": [[44, "references"]], "SDCFlows": [[41, null]], "Sampling that brain and MRI": [[45, "Sampling-that-brain-and-MRI"]], "See Also": [[18, null]], "Standalone command line usage": [[39, null]], "Submodules": [[1, "submodules"], [8, "submodules"], [16, "submodules"], [24, "submodules"], [26, "submodules"], [28, "submodules"], [32, "submodules"]], "Subpackages": [[26, "subpackages"]], "Susceptibility Distortions in a nutshell": [[45, null]], "Thanks": [[18, null]], "The B_\\text{0} field is not absolutely uniform": [[45, "The-B_\\text{0}-field-is-not-absolutely-uniform"]], "The effect if the PE direction is reversed (\u201cnegative blips\u201d)": [[45, "The-effect-if-the-PE-direction-is-reversed-(%22negative-blips%22)"]], "The effects of this physical phenomenon": [[45, "The-effects-of-this-physical-phenomenon"]], "The second ingredient of the distortion cocktail - acquisition trade-offs": [[45, "The-second-ingredient-of-the-distortion-cocktail---acquisition-trade-offs"]], "Unwarping the distorted data": [[44, "unwarping-the-distorted-data"]], "Usage": [[5, "usage"]], "What\u2019s new?": [[38, null]], "sdcflows.cli package": [[1, null]], "sdcflows.cli.main module": [[2, null]], "sdcflows.cli.parser module": [[3, null]], "sdcflows.cli.workflow module": [[4, null]], "sdcflows.config module": [[5, null]], "sdcflows.data package": [[6, null]], "sdcflows.fieldmaps module": [[7, null]], "sdcflows.interfaces package": [[8, null]], "sdcflows.interfaces.brainmask module": [[9, null]], "sdcflows.interfaces.bspline module": [[10, null]], "sdcflows.interfaces.epi module": [[11, null]], "sdcflows.interfaces.fmap module": [[12, null]], "sdcflows.interfaces.reportlets module": [[13, null]], "sdcflows.interfaces.utils module": [[14, null]], "sdcflows.transform module": [[15, null]], "sdcflows.utils package": [[16, null]], "sdcflows.utils.bimap module": [[17, null]], "sdcflows.utils.epimanip module": [[18, null]], "sdcflows.utils.misc module": [[19, null]], "sdcflows.utils.phasemanip module": [[20, null]], "sdcflows.utils.telemetry module": [[21, null]], "sdcflows.utils.tools module": [[22, null]], "sdcflows.utils.wrangler module": [[23, null]], "sdcflows.viz package": [[24, null]], "sdcflows.viz.utils module": [[25, null]], "sdcflows.workflows package": [[26, null]], "sdcflows.workflows.ancillary module": [[27, null]], "sdcflows.workflows.apply package": [[28, null]], "sdcflows.workflows.apply.correction module": [[29, null]], "sdcflows.workflows.apply.registration module": [[30, null]], "sdcflows.workflows.base module": [[31, null]], "sdcflows.workflows.fit package": [[32, null]], "sdcflows.workflows.fit.base module": [[33, null]], "sdcflows.workflows.fit.fieldmap module": [[34, null]], "sdcflows.workflows.fit.pepolar module": [[35, null]], "sdcflows.workflows.fit.syn module": [[36, null]], "sdcflows.workflows.outputs module": [[37, null]]}, "docnames": ["api", "api/sdcflows.cli", "api/sdcflows.cli.main", "api/sdcflows.cli.parser", "api/sdcflows.cli.workflow", "api/sdcflows.config", "api/sdcflows.data", "api/sdcflows.fieldmaps", "api/sdcflows.interfaces", "api/sdcflows.interfaces.brainmask", "api/sdcflows.interfaces.bspline", "api/sdcflows.interfaces.epi", "api/sdcflows.interfaces.fmap", "api/sdcflows.interfaces.reportlets", "api/sdcflows.interfaces.utils", "api/sdcflows.transform", "api/sdcflows.utils", "api/sdcflows.utils.bimap", "api/sdcflows.utils.epimanip", "api/sdcflows.utils.misc", "api/sdcflows.utils.phasemanip", "api/sdcflows.utils.telemetry", "api/sdcflows.utils.tools", "api/sdcflows.utils.wrangler", "api/sdcflows.viz", "api/sdcflows.viz.utils", "api/sdcflows.workflows", "api/sdcflows.workflows.ancillary", "api/sdcflows.workflows.apply", "api/sdcflows.workflows.apply.correction", "api/sdcflows.workflows.apply.registration", "api/sdcflows.workflows.base", "api/sdcflows.workflows.fit", "api/sdcflows.workflows.fit.base", "api/sdcflows.workflows.fit.fieldmap", "api/sdcflows.workflows.fit.pepolar", "api/sdcflows.workflows.fit.syn", "api/sdcflows.workflows.outputs", "changes", "cli", "examples", "index", "installation", "links", "methods", "notebooks/SDC - Theory and physics"], "envversion": {"nbsphinx": 4, "sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1}, "filenames": ["api.rst", "api/sdcflows.cli.rst", "api/sdcflows.cli.main.rst", "api/sdcflows.cli.parser.rst", "api/sdcflows.cli.workflow.rst", "api/sdcflows.config.rst", "api/sdcflows.data.rst", "api/sdcflows.fieldmaps.rst", "api/sdcflows.interfaces.rst", "api/sdcflows.interfaces.brainmask.rst", "api/sdcflows.interfaces.bspline.rst", "api/sdcflows.interfaces.epi.rst", "api/sdcflows.interfaces.fmap.rst", "api/sdcflows.interfaces.reportlets.rst", "api/sdcflows.interfaces.utils.rst", "api/sdcflows.transform.rst", "api/sdcflows.utils.rst", "api/sdcflows.utils.bimap.rst", "api/sdcflows.utils.epimanip.rst", "api/sdcflows.utils.misc.rst", "api/sdcflows.utils.phasemanip.rst", "api/sdcflows.utils.telemetry.rst", "api/sdcflows.utils.tools.rst", "api/sdcflows.utils.wrangler.rst", "api/sdcflows.viz.rst", "api/sdcflows.viz.utils.rst", "api/sdcflows.workflows.rst", "api/sdcflows.workflows.ancillary.rst", "api/sdcflows.workflows.apply.rst", "api/sdcflows.workflows.apply.correction.rst", "api/sdcflows.workflows.apply.registration.rst", "api/sdcflows.workflows.base.rst", "api/sdcflows.workflows.fit.rst", "api/sdcflows.workflows.fit.base.rst", "api/sdcflows.workflows.fit.fieldmap.rst", "api/sdcflows.workflows.fit.pepolar.rst", "api/sdcflows.workflows.fit.syn.rst", "api/sdcflows.workflows.outputs.rst", "changes.rst", "cli.rst", "examples.rst", "index.rst", "installation.rst", "links.rst", "methods.rst", "notebooks/SDC - Theory and physics.ipynb"], "indexentries": {"add() (sdcflows.utils.bimap.bidict method)": [[17, "sdcflows.utils.bimap.bidict.add", false]], "analysis_level (sdcflows.config.workflow attribute)": [[5, "sdcflows.config.workflow.analysis_level", false]], "ants_float (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.ants_float", false]], "apply() (sdcflows.transform.b0fieldtransform method)": [[15, "sdcflows.transform.B0FieldTransform.apply", false]], "applycoeffsfield (class in sdcflows.interfaces.bspline)": [[10, "sdcflows.interfaces.bspline.ApplyCoeffsField", false]], "as_path() (sdcflows.data.load method)": [[6, "sdcflows.data.load.as_path", false]], "as_path() (sdcflows.data.loader method)": [[6, "sdcflows.data.Loader.as_path", false]], "au2rads() (in module sdcflows.utils.phasemanip)": [[20, "sdcflows.utils.phasemanip.au2rads", false]], "b0fieldtransform (class in sdcflows.transform)": [[15, "sdcflows.transform.B0FieldTransform", false]], "bidict (class in sdcflows.utils.bimap)": [[17, "sdcflows.utils.bimap.bidict", false]], "bids_database_dir (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.bids_database_dir", false]], "bids_database_wipe (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.bids_database_wipe", false]], "bids_description_hash (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.bids_description_hash", false]], "bids_dir (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.bids_dir", false]], "bids_filters (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.bids_filters", false]], "bids_id (sdcflows.fieldmaps.fieldmapestimation attribute)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.bids_id", false]], "bids_root (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.bids_root", false]], "binarydilation (class in sdcflows.interfaces.brainmask)": [[9, "sdcflows.interfaces.brainmask.BinaryDilation", false]], "brain_masker() (in module sdcflows.utils.tools)": [[22, "sdcflows.utils.tools.brain_masker", false]], "brainextraction (class in sdcflows.interfaces.brainmask)": [[9, "sdcflows.interfaces.brainmask.BrainExtraction", false]], "bspline_grid() (in module sdcflows.interfaces.bspline)": [[10, "sdcflows.interfaces.bspline.bspline_grid", false]], "bsplineapprox (class in sdcflows.interfaces.bspline)": [[10, "sdcflows.interfaces.bspline.BSplineApprox", false]], "build_workflow() (in module sdcflows.cli.workflow)": [[4, "sdcflows.cli.workflow.build_workflow", false]], "cached() (sdcflows.data.load method)": [[6, "sdcflows.data.load.cached", false]], "cached() (sdcflows.data.loader method)": [[6, "sdcflows.data.Loader.cached", false]], "check_path() (sdcflows.fieldmaps.fieldmapfile method)": [[7, "sdcflows.fieldmaps.FieldmapFile.check_path", false]], "checkb0units (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.CheckB0Units", false]], "checkregister (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.CheckRegister", false]], "clear() (sdcflows.utils.bimap.bidict method)": [[17, "sdcflows.utils.bimap.bidict.clear", false]], "clear_registry() (in module sdcflows.fieldmaps)": [[7, "sdcflows.fieldmaps.clear_registry", false]], "cli (sdcflows.config.loggers attribute)": [[5, "sdcflows.config.loggers.cli", false]], "coeffs (sdcflows.transform.b0fieldtransform attribute)": [[15, "sdcflows.transform.B0FieldTransform.coeffs", false]], "convertwarp (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.ConvertWarp", false]], "coolwarm_transparent() (in module sdcflows.viz.utils)": [[25, "sdcflows.viz.utils.coolwarm_transparent", false]], "cpu_count (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.cpu_count", false]], "crashfile_format (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.crashfile_format", false]], "cwd (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.cwd", false]], "debug (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.debug", false]], "default (sdcflows.config.loggers attribute)": [[5, "sdcflows.config.loggers.default", false]], "delta_te() (in module sdcflows.utils.phasemanip)": [[20, "sdcflows.utils.phasemanip.delta_te", false]], "denoiseimage (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.DenoiseImage", false]], "deoblique (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.Deoblique", false]], "deoblique_and_zooms() (in module sdcflows.utils.tools)": [[22, "sdcflows.utils.tools.deoblique_and_zooms", false]], "derivativesdatasink (class in sdcflows.workflows.outputs)": [[37, "sdcflows.workflows.outputs.DerivativesDataSink", false]], "disp_to_fmap() (in module sdcflows.transform)": [[15, "sdcflows.transform.disp_to_fmap", false]], "displacementsfield2fieldmap (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.DisplacementsField2Fieldmap", false]], "dry_run (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.dry_run", false]], "dumps() (in module sdcflows.config)": [[5, "sdcflows.config.dumps", false]], "ensure_positive_cosines() (in module sdcflows.utils.tools)": [[22, "sdcflows.utils.tools.ensure_positive_cosines", false]], "entities (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.entities", false]], "environment (class in sdcflows.config)": [[5, "sdcflows.config.environment", false]], "epi_mask() (in module sdcflows.utils.epimanip)": [[18, "sdcflows.utils.epimanip.epi_mask", false]], "estimatorregistry (class in sdcflows.utils.bimap)": [[17, "sdcflows.utils.bimap.EstimatorRegistry", false]], "estimatortype (class in sdcflows.fieldmaps)": [[7, "sdcflows.fieldmaps.EstimatorType", false]], "exec_docker_version (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.exec_docker_version", false]], "exec_env (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.exec_env", false]], "execution (class in sdcflows.config)": [[5, "sdcflows.config.execution", false]], "fieldmapestimation (class in sdcflows.fieldmaps)": [[7, "sdcflows.fieldmaps.FieldmapEstimation", false]], "fieldmapfile (class in sdcflows.fieldmaps)": [[7, "sdcflows.fieldmaps.FieldmapFile", false]], "fieldmapreportlet (class in sdcflows.interfaces.reportlets)": [[13, "sdcflows.interfaces.reportlets.FieldmapReportlet", false]], "file_path (in module sdcflows.config)": [[5, "sdcflows.config.file_path", false]], "find_anatomical_estimators() (in module sdcflows.utils.wrangler)": [[23, "sdcflows.utils.wrangler.find_anatomical_estimators", false]], "find_estimators() (in module sdcflows.utils.wrangler)": [[23, "sdcflows.utils.wrangler.find_estimators", false]], "find_meta (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.find_meta", false]], "fit() (sdcflows.transform.b0fieldtransform method)": [[15, "sdcflows.transform.B0FieldTransform.fit", false]], "flatten (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.Flatten", false]], "fmap_to_disp() (in module sdcflows.transform)": [[15, "sdcflows.transform.fmap_to_disp", false]], "fmapless (sdcflows.config.workflow attribute)": [[5, "sdcflows.config.workflow.fmapless", false]], "free_mem (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.free_mem", false]], "from_dict() (in module sdcflows.config)": [[5, "sdcflows.config.from_dict", false]], "front() (in module sdcflows.utils.misc)": [[19, "sdcflows.utils.misc.front", false]], "get() (in module sdcflows.config)": [[5, "sdcflows.config.get", false]], "get_free_mem() (in module sdcflows.utils.misc)": [[19, "sdcflows.utils.misc.get_free_mem", false]], "get_identifier() (in module sdcflows.fieldmaps)": [[7, "sdcflows.fieldmaps.get_identifier", false]], "get_key() (sdcflows.utils.bimap.estimatorregistry method)": [[17, "sdcflows.utils.bimap.EstimatorRegistry.get_key", false]], "get_linked_libs (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.get_linked_libs", false]], "get_plugin() (sdcflows.config.nipype class method)": [[5, "sdcflows.config.nipype.get_plugin", false]], "get_trt() (in module sdcflows.utils.epimanip)": [[18, "sdcflows.utils.epimanip.get_trt", false]], "get_workflow() (sdcflows.fieldmaps.fieldmapestimation method)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.get_workflow", false]], "getlogger() (sdcflows.config.loggers class method)": [[5, "sdcflows.config.loggers.getLogger", false]], "getreadouttime (class in sdcflows.interfaces.epi)": [[11, "sdcflows.interfaces.epi.GetReadoutTime", false]], "grid_bspline_weights() (in module sdcflows.transform)": [[15, "sdcflows.transform.grid_bspline_weights", false]], "init() (sdcflows.config.execution class method)": [[5, "sdcflows.config.execution.init", false]], "init() (sdcflows.config.loggers class method)": [[5, "sdcflows.config.loggers.init", false]], "init() (sdcflows.config.nipype class method)": [[5, "sdcflows.config.nipype.init", false]], "init_3dqwarp_wf() (in module sdcflows.workflows.fit.pepolar)": [[35, "sdcflows.workflows.fit.pepolar.init_3dQwarp_wf", false]], "init_brainextraction_wf() (in module sdcflows.workflows.ancillary)": [[27, "sdcflows.workflows.ancillary.init_brainextraction_wf", false]], "init_coeff2epi_wf() (in module sdcflows.workflows.apply.registration)": [[30, "sdcflows.workflows.apply.registration.init_coeff2epi_wf", false]], "init_fmap_derivatives_wf() (in module sdcflows.workflows.outputs)": [[37, "sdcflows.workflows.outputs.init_fmap_derivatives_wf", false]], "init_fmap_preproc_wf() (in module sdcflows.workflows.base)": [[31, "sdcflows.workflows.base.init_fmap_preproc_wf", false]], "init_fmap_reports_wf() (in module sdcflows.workflows.outputs)": [[37, "sdcflows.workflows.outputs.init_fmap_reports_wf", false]], "init_fmap_wf() (in module sdcflows.workflows.fit.fieldmap)": [[34, "sdcflows.workflows.fit.fieldmap.init_fmap_wf", false]], "init_magnitude_wf() (in module sdcflows.workflows.fit.fieldmap)": [[34, "sdcflows.workflows.fit.fieldmap.init_magnitude_wf", false]], "init_phdiff_wf() (in module sdcflows.workflows.fit.fieldmap)": [[34, "sdcflows.workflows.fit.fieldmap.init_phdiff_wf", false]], "init_sdcflows_wf() (in module sdcflows.workflows.fit.base)": [[33, "sdcflows.workflows.fit.base.init_sdcflows_wf", false]], "init_syn_preprocessing_wf() (in module sdcflows.workflows.fit.syn)": [[36, "sdcflows.workflows.fit.syn.init_syn_preprocessing_wf", false]], "init_syn_sdc_wf() (in module sdcflows.workflows.fit.syn)": [[36, "sdcflows.workflows.fit.syn.init_syn_sdc_wf", false]], "init_topup_wf() (in module sdcflows.workflows.fit.pepolar)": [[35, "sdcflows.workflows.fit.pepolar.init_topup_wf", false]], "init_unwarp_wf() (in module sdcflows.workflows.apply.correction)": [[29, "sdcflows.workflows.apply.correction.init_unwarp_wf", false]], "interface (sdcflows.config.loggers attribute)": [[5, "sdcflows.config.loggers.interface", false]], "last() (in module sdcflows.utils.misc)": [[19, "sdcflows.utils.misc.last", false]], "layout (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.layout", false]], "load() (in module sdcflows.config)": [[5, "sdcflows.config.load", false]], "load() (in module sdcflows.data)": [[6, "sdcflows.data.load", false]], "loader (class in sdcflows.data)": [[6, "sdcflows.data.Loader", false]], "local_hash_check (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.local_hash_check", false]], "log_dir (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.log_dir", false]], "log_level (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.log_level", false]], "loggers (class in sdcflows.config)": [[5, "sdcflows.config.loggers", false]], "main() (in module sdcflows.cli.main)": [[2, "sdcflows.cli.main.main", false]], "mapped (sdcflows.transform.b0fieldtransform attribute)": [[15, "sdcflows.transform.B0FieldTransform.mapped", false]], "match_histogram() (in module sdcflows.workflows.fit.syn)": [[36, "sdcflows.workflows.fit.syn.match_histogram", false]], "memory_gb (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.memory_gb", false]], "metadata (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.metadata", false]], "metadataerror": [[7, "sdcflows.fieldmaps.MetadataError", false]], "method (sdcflows.fieldmaps.fieldmapestimation attribute)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.method", false]], "module": [[1, "module-sdcflows.cli", false], [2, "module-sdcflows.cli.main", false], [3, "module-sdcflows.cli.parser", false], [4, "module-sdcflows.cli.workflow", false], [5, "module-sdcflows.config", false], [6, "module-sdcflows.data", false], [7, "module-sdcflows.fieldmaps", false], [8, "module-sdcflows.interfaces", false], [9, "module-sdcflows.interfaces.brainmask", false], [10, "module-sdcflows.interfaces.bspline", false], [11, "module-sdcflows.interfaces.epi", false], [12, "module-sdcflows.interfaces.fmap", false], [13, "module-sdcflows.interfaces.reportlets", false], [14, "module-sdcflows.interfaces.utils", false], [15, "module-sdcflows.transform", false], [16, "module-sdcflows.utils", false], [17, "module-sdcflows.utils.bimap", false], [18, "module-sdcflows.utils.epimanip", false], [19, "module-sdcflows.utils.misc", false], [20, "module-sdcflows.utils.phasemanip", false], [21, "module-sdcflows.utils.telemetry", false], [22, "module-sdcflows.utils.tools", false], [23, "module-sdcflows.utils.wrangler", false], [24, "module-sdcflows.viz", false], [25, "module-sdcflows.viz.utils", false], [26, "module-sdcflows.workflows", false], [27, "module-sdcflows.workflows.ancillary", false], [28, "module-sdcflows.workflows.apply", false], [29, "module-sdcflows.workflows.apply.correction", false], [30, "module-sdcflows.workflows.apply.registration", false], [31, "module-sdcflows.workflows.base", false], [32, "module-sdcflows.workflows.fit", false], [33, "module-sdcflows.workflows.fit.base", false], [34, "module-sdcflows.workflows.fit.fieldmap", false], [35, "module-sdcflows.workflows.fit.pepolar", false], [36, "module-sdcflows.workflows.fit.syn", false], [37, "module-sdcflows.workflows.outputs", false]], "nipype (class in sdcflows.config)": [[5, "sdcflows.config.nipype", false]], "nipype_version (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.nipype_version", false]], "notrack (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.notrack", false]], "nprocs (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.nprocs", false]], "omp_nthreads (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.omp_nthreads", false]], "output_dir (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.output_dir", false]], "overcommit_limit (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.overcommit_limit", false]], "overcommit_policy (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.overcommit_policy", false]], "padslices (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.PadSlices", false]], "parse_args() (in module sdcflows.cli.parser)": [[3, "sdcflows.cli.parser.parse_args", false]], "participant_label (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.participant_label", false]], "path (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.path", false]], "paths() (sdcflows.fieldmaps.fieldmapestimation method)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.paths", false]], "pdb (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.pdb", false]], "phasediff2fieldmap (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.Phasediff2Fieldmap", false]], "phasemap2rads (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.PhaseMap2rads", false]], "phdiff2fmap() (in module sdcflows.utils.phasemanip)": [[20, "sdcflows.utils.phasemanip.phdiff2fmap", false]], "plot_registration() (in module sdcflows.viz.utils)": [[25, "sdcflows.viz.utils.plot_registration", false]], "plugin (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.plugin", false]], "plugin_args (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.plugin_args", false]], "positivedirectioncosines (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.PositiveDirectionCosines", false]], "readable() (sdcflows.data.load method)": [[6, "sdcflows.data.load.readable", false]], "readable() (sdcflows.data.loader method)": [[6, "sdcflows.data.Loader.readable", false]], "remove_node_directories (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.remove_node_directories", false]], "reoblique (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.Reoblique", false]], "reorient_pedir() (in module sdcflows.utils.tools)": [[22, "sdcflows.utils.tools.reorient_pedir", false]], "reorientimageandmetadata (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.ReorientImageAndMetadata", false]], "resample_to_zooms() (in module sdcflows.utils.tools)": [[22, "sdcflows.utils.tools.resample_to_zooms", false]], "resource_monitor (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.resource_monitor", false]], "restore_env() (in module sdcflows.config)": [[5, "sdcflows.config.restore_env", false]], "run_uuid (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.run_uuid", false]], "sanitized_id (sdcflows.fieldmaps.fieldmapestimation attribute)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.sanitized_id", false]], "sdcflows.cli": [[1, "module-sdcflows.cli", false]], "sdcflows.cli.main": [[2, "module-sdcflows.cli.main", false]], "sdcflows.cli.parser": [[3, "module-sdcflows.cli.parser", false]], "sdcflows.cli.workflow": [[4, "module-sdcflows.cli.workflow", false]], "sdcflows.config": [[5, "module-sdcflows.config", false]], "sdcflows.data": [[6, "module-sdcflows.data", false]], "sdcflows.fieldmaps": [[7, "module-sdcflows.fieldmaps", false]], "sdcflows.interfaces": [[8, "module-sdcflows.interfaces", false]], "sdcflows.interfaces.brainmask": [[9, "module-sdcflows.interfaces.brainmask", false]], "sdcflows.interfaces.bspline": [[10, "module-sdcflows.interfaces.bspline", false]], "sdcflows.interfaces.epi": [[11, "module-sdcflows.interfaces.epi", false]], "sdcflows.interfaces.fmap": [[12, "module-sdcflows.interfaces.fmap", false]], "sdcflows.interfaces.reportlets": [[13, "module-sdcflows.interfaces.reportlets", false]], "sdcflows.interfaces.utils": [[14, "module-sdcflows.interfaces.utils", false]], "sdcflows.transform": [[15, "module-sdcflows.transform", false]], "sdcflows.utils": [[16, "module-sdcflows.utils", false]], "sdcflows.utils.bimap": [[17, "module-sdcflows.utils.bimap", false]], "sdcflows.utils.epimanip": [[18, "module-sdcflows.utils.epimanip", false]], "sdcflows.utils.misc": [[19, "module-sdcflows.utils.misc", false]], "sdcflows.utils.phasemanip": [[20, "module-sdcflows.utils.phasemanip", false]], "sdcflows.utils.telemetry": [[21, "module-sdcflows.utils.telemetry", false]], "sdcflows.utils.tools": [[22, "module-sdcflows.utils.tools", false]], "sdcflows.utils.wrangler": [[23, "module-sdcflows.utils.wrangler", false]], "sdcflows.viz": [[24, "module-sdcflows.viz", false]], "sdcflows.viz.utils": [[25, "module-sdcflows.viz.utils", false]], "sdcflows.workflows": [[26, "module-sdcflows.workflows", false]], "sdcflows.workflows.ancillary": [[27, "module-sdcflows.workflows.ancillary", false]], "sdcflows.workflows.apply": [[28, "module-sdcflows.workflows.apply", false]], "sdcflows.workflows.apply.correction": [[29, "module-sdcflows.workflows.apply.correction", false]], "sdcflows.workflows.apply.registration": [[30, "module-sdcflows.workflows.apply.registration", false]], "sdcflows.workflows.base": [[31, "module-sdcflows.workflows.base", false]], "sdcflows.workflows.fit": [[32, "module-sdcflows.workflows.fit", false]], "sdcflows.workflows.fit.base": [[33, "module-sdcflows.workflows.fit.base", false]], "sdcflows.workflows.fit.fieldmap": [[34, "module-sdcflows.workflows.fit.fieldmap", false]], "sdcflows.workflows.fit.pepolar": [[35, "module-sdcflows.workflows.fit.pepolar", false]], "sdcflows.workflows.fit.syn": [[36, "module-sdcflows.workflows.fit.syn", false]], "sdcflows.workflows.outputs": [[37, "module-sdcflows.workflows.outputs", false]], "send_crumb() (in module sdcflows.utils.telemetry)": [[21, "sdcflows.utils.telemetry.send_crumb", false]], "session_label (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.session_label", false]], "setup_migas() (in module sdcflows.utils.telemetry)": [[21, "sdcflows.utils.telemetry.setup_migas", false]], "sloppy (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.sloppy", false]], "sortpeblips (class in sdcflows.interfaces.epi)": [[11, "sdcflows.interfaces.epi.SortPEBlips", false]], "sources (sdcflows.fieldmaps.fieldmapestimation attribute)": [[7, "sdcflows.fieldmaps.FieldmapEstimation.sources", false]], "sources (sdcflows.utils.bimap.estimatorregistry property)": [[17, "sdcflows.utils.bimap.EstimatorRegistry.sources", false]], "species (sdcflows.config.workflow attribute)": [[5, "sdcflows.config.workflow.species", false]], "stop_on_first_crash (sdcflows.config.nipype attribute)": [[5, "sdcflows.config.nipype.stop_on_first_crash", false]], "subtract_phases() (in module sdcflows.utils.phasemanip)": [[20, "sdcflows.utils.phasemanip.subtract_phases", false]], "subtractphases (class in sdcflows.interfaces.fmap)": [[12, "sdcflows.interfaces.fmap.SubtractPhases", false]], "suffix (sdcflows.fieldmaps.fieldmapfile attribute)": [[7, "sdcflows.fieldmaps.FieldmapFile.suffix", false]], "template_id (sdcflows.config.workflow attribute)": [[5, "sdcflows.config.workflow.template_id", false]], "templateflow_home (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.templateflow_home", false]], "templateflow_version (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.templateflow_version", false]], "to_displacements() (sdcflows.transform.b0fieldtransform method)": [[15, "sdcflows.transform.B0FieldTransform.to_displacements", false]], "to_filename() (in module sdcflows.config)": [[5, "sdcflows.config.to_filename", false]], "topupcoeffreorient (class in sdcflows.interfaces.bspline)": [[10, "sdcflows.interfaces.bspline.TOPUPCoeffReorient", false]], "total_memory (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.total_memory", false]], "transformcoefficients (class in sdcflows.interfaces.bspline)": [[10, "sdcflows.interfaces.bspline.TransformCoefficients", false]], "uniformgrid (class in sdcflows.interfaces.utils)": [[14, "sdcflows.interfaces.utils.UniformGrid", false]], "union (class in sdcflows.interfaces.brainmask)": [[9, "sdcflows.interfaces.brainmask.Union", false]], "unwarp_parallel() (in module sdcflows.transform)": [[15, "sdcflows.transform.unwarp_parallel", false]], "utils (sdcflows.config.loggers attribute)": [[5, "sdcflows.config.loggers.utils", false]], "version (sdcflows.config.environment attribute)": [[5, "sdcflows.config.environment.version", false]], "work_dir (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.work_dir", false]], "worker() (in module sdcflows.transform)": [[15, "sdcflows.transform.worker", false]], "workflow (class in sdcflows.config)": [[5, "sdcflows.config.workflow", false]], "workflow (sdcflows.config.loggers attribute)": [[5, "sdcflows.config.loggers.workflow", false]], "write_graph (sdcflows.config.execution attribute)": [[5, "sdcflows.config.execution.write_graph", false]]}, "objects": {"sdcflows": [[1, 0, 0, "-", "cli"], [5, 0, 0, "-", "config"], [6, 0, 0, "-", "data"], [7, 0, 0, "-", "fieldmaps"], [8, 0, 0, "-", "interfaces"], [15, 0, 0, "-", "transform"], [16, 0, 0, "-", "utils"], [24, 0, 0, "-", "viz"], [26, 0, 0, "-", "workflows"]], "sdcflows.cli": [[2, 0, 0, "-", "main"], [3, 0, 0, "-", "parser"], [4, 0, 0, "-", "workflow"]], "sdcflows.cli.main": [[2, 1, 1, "", "main"]], "sdcflows.cli.parser": [[3, 1, 1, "", "parse_args"]], "sdcflows.cli.workflow": [[4, 1, 1, "", "build_workflow"]], "sdcflows.config": [[5, 1, 1, "", "dumps"], [5, 2, 1, "", "environment"], [5, 2, 1, "", "execution"], [5, 5, 1, "", "file_path"], [5, 1, 1, "", "from_dict"], [5, 1, 1, "", "get"], [5, 1, 1, "", "load"], [5, 2, 1, "", "loggers"], [5, 2, 1, "", "nipype"], [5, 1, 1, "", "restore_env"], [5, 1, 1, "", "to_filename"], [5, 2, 1, "", "workflow"]], "sdcflows.config.environment": [[5, 3, 1, "", "cpu_count"], [5, 3, 1, "", "exec_docker_version"], [5, 3, 1, "", "exec_env"], [5, 3, 1, "", "free_mem"], [5, 3, 1, "", "nipype_version"], [5, 3, 1, "", "overcommit_limit"], [5, 3, 1, "", "overcommit_policy"], [5, 3, 1, "", "templateflow_version"], [5, 3, 1, "", "total_memory"], [5, 3, 1, "", "version"]], "sdcflows.config.execution": [[5, 3, 1, "", "ants_float"], [5, 3, 1, "", "bids_database_dir"], [5, 3, 1, "", "bids_database_wipe"], [5, 3, 1, "", "bids_description_hash"], [5, 3, 1, "", "bids_dir"], [5, 3, 1, "", "bids_filters"], [5, 3, 1, "", "cwd"], [5, 3, 1, "", "debug"], [5, 3, 1, "", "dry_run"], [5, 4, 1, "", "init"], [5, 3, 1, "", "layout"], [5, 3, 1, "", "log_dir"], [5, 3, 1, "", "log_level"], [5, 3, 1, "", "notrack"], [5, 3, 1, "", "output_dir"], [5, 3, 1, "", "participant_label"], [5, 3, 1, "", "pdb"], [5, 3, 1, "", "run_uuid"], [5, 3, 1, "", "session_label"], [5, 3, 1, "", "sloppy"], [5, 3, 1, "", "templateflow_home"], [5, 3, 1, "", "work_dir"], [5, 3, 1, "", "write_graph"]], "sdcflows.config.loggers": [[5, 3, 1, "", "cli"], [5, 3, 1, "", "default"], [5, 4, 1, "", "getLogger"], [5, 4, 1, "", "init"], [5, 3, 1, "", "interface"], [5, 3, 1, "", "utils"], [5, 3, 1, "", "workflow"]], "sdcflows.config.nipype": [[5, 3, 1, "", "crashfile_format"], [5, 3, 1, "", "get_linked_libs"], [5, 4, 1, "", "get_plugin"], [5, 4, 1, "", "init"], [5, 3, 1, "", "local_hash_check"], [5, 3, 1, "", "memory_gb"], [5, 3, 1, "", "nprocs"], [5, 3, 1, "", "omp_nthreads"], [5, 3, 1, "", "plugin"], [5, 3, 1, "", "plugin_args"], [5, 3, 1, "", "remove_node_directories"], [5, 3, 1, "", "resource_monitor"], [5, 3, 1, "", "stop_on_first_crash"]], "sdcflows.config.workflow": [[5, 3, 1, "", "analysis_level"], [5, 3, 1, "", "fmapless"], [5, 3, 1, "", "species"], [5, 3, 1, "", "template_id"]], "sdcflows.data": [[6, 2, 1, "", "Loader"], [6, 1, 1, "", "load"]], "sdcflows.data.Loader": [[6, 4, 1, "", "as_path"], [6, 4, 1, "", "cached"], [6, 4, 1, "", "readable"]], "sdcflows.data.load": [[6, 4, 1, "", "as_path"], [6, 4, 1, "", "cached"], [6, 4, 1, "", "readable"]], "sdcflows.fieldmaps": [[7, 2, 1, "", "EstimatorType"], [7, 2, 1, "", "FieldmapEstimation"], [7, 2, 1, "", "FieldmapFile"], [7, 6, 1, "", "MetadataError"], [7, 1, 1, "", "clear_registry"], [7, 1, 1, "", "get_identifier"]], "sdcflows.fieldmaps.FieldmapEstimation": [[7, 3, 1, "", "bids_id"], [7, 4, 1, "", "get_workflow"], [7, 3, 1, "", "method"], [7, 4, 1, "", "paths"], [7, 3, 1, "", "sanitized_id"], [7, 3, 1, "", "sources"]], "sdcflows.fieldmaps.FieldmapFile": [[7, 3, 1, "", "bids_root"], [7, 4, 1, "", "check_path"], [7, 3, 1, "", "entities"], [7, 3, 1, "", "find_meta"], [7, 3, 1, "", "metadata"], [7, 3, 1, "", "path"], [7, 3, 1, "", "suffix"]], "sdcflows.interfaces": [[9, 0, 0, "-", "brainmask"], [10, 0, 0, "-", "bspline"], [11, 0, 0, "-", "epi"], [12, 0, 0, "-", "fmap"], [13, 0, 0, "-", "reportlets"], [14, 0, 0, "-", "utils"]], "sdcflows.interfaces.brainmask": [[9, 2, 1, "", "BinaryDilation"], [9, 2, 1, "", "BrainExtraction"], [9, 2, 1, "", "Union"]], "sdcflows.interfaces.bspline": [[10, 2, 1, "", "ApplyCoeffsField"], [10, 2, 1, "", "BSplineApprox"], [10, 2, 1, "", "TOPUPCoeffReorient"], [10, 2, 1, "", "TransformCoefficients"], [10, 1, 1, "", "bspline_grid"]], "sdcflows.interfaces.epi": [[11, 2, 1, "", "GetReadoutTime"], [11, 2, 1, "", "SortPEBlips"]], "sdcflows.interfaces.fmap": [[12, 2, 1, "", "CheckB0Units"], [12, 2, 1, "", "CheckRegister"], [12, 2, 1, "", "DisplacementsField2Fieldmap"], [12, 2, 1, "", "PhaseMap2rads"], [12, 2, 1, "", "Phasediff2Fieldmap"], [12, 2, 1, "", "SubtractPhases"]], "sdcflows.interfaces.reportlets": [[13, 2, 1, "", "FieldmapReportlet"]], "sdcflows.interfaces.utils": [[14, 2, 1, "", "ConvertWarp"], [14, 2, 1, "", "DenoiseImage"], [14, 2, 1, "", "Deoblique"], [14, 2, 1, "", "Flatten"], [14, 2, 1, "", "PadSlices"], [14, 2, 1, "", "PositiveDirectionCosines"], [14, 2, 1, "", "Reoblique"], [14, 2, 1, "", "ReorientImageAndMetadata"], [14, 2, 1, "", "UniformGrid"]], "sdcflows.transform": [[15, 2, 1, "", "B0FieldTransform"], [15, 1, 1, "", "disp_to_fmap"], [15, 1, 1, "", "fmap_to_disp"], [15, 1, 1, "", "grid_bspline_weights"], [15, 1, 1, "", "unwarp_parallel"], [15, 1, 1, "", "worker"]], "sdcflows.transform.B0FieldTransform": [[15, 4, 1, "", "apply"], [15, 3, 1, "", "coeffs"], [15, 4, 1, "", "fit"], [15, 3, 1, "", "mapped"], [15, 4, 1, "", "to_displacements"]], "sdcflows.utils": [[17, 0, 0, "-", "bimap"], [18, 0, 0, "-", "epimanip"], [19, 0, 0, "-", "misc"], [20, 0, 0, "-", "phasemanip"], [21, 0, 0, "-", "telemetry"], [22, 0, 0, "-", "tools"], [23, 0, 0, "-", "wrangler"]], "sdcflows.utils.bimap": [[17, 2, 1, "", "EstimatorRegistry"], [17, 2, 1, "", "bidict"]], "sdcflows.utils.bimap.EstimatorRegistry": [[17, 4, 1, "", "get_key"], [17, 7, 1, "", "sources"]], "sdcflows.utils.bimap.bidict": [[17, 4, 1, "", "add"], [17, 4, 1, "", "clear"]], "sdcflows.utils.epimanip": [[18, 1, 1, "", "epi_mask"], [18, 1, 1, "", "get_trt"]], "sdcflows.utils.misc": [[19, 1, 1, "", "front"], [19, 1, 1, "", "get_free_mem"], [19, 1, 1, "", "last"]], "sdcflows.utils.phasemanip": [[20, 1, 1, "", "au2rads"], [20, 1, 1, "", "delta_te"], [20, 1, 1, "", "phdiff2fmap"], [20, 1, 1, "", "subtract_phases"]], "sdcflows.utils.telemetry": [[21, 1, 1, "", "send_crumb"], [21, 1, 1, "", "setup_migas"]], "sdcflows.utils.tools": [[22, 1, 1, "", "brain_masker"], [22, 1, 1, "", "deoblique_and_zooms"], [22, 1, 1, "", "ensure_positive_cosines"], [22, 1, 1, "", "reorient_pedir"], [22, 1, 1, "", "resample_to_zooms"]], "sdcflows.utils.wrangler": [[23, 1, 1, "", "find_anatomical_estimators"], [23, 1, 1, "", "find_estimators"]], "sdcflows.viz": [[25, 0, 0, "-", "utils"]], "sdcflows.viz.utils": [[25, 1, 1, "", "coolwarm_transparent"], [25, 1, 1, "", "plot_registration"]], "sdcflows.workflows": [[27, 0, 0, "-", "ancillary"], [28, 0, 0, "-", "apply"], [31, 0, 0, "-", "base"], [32, 0, 0, "-", "fit"], [37, 0, 0, "-", "outputs"]], "sdcflows.workflows.ancillary": [[27, 1, 1, "", "init_brainextraction_wf"]], "sdcflows.workflows.apply": [[29, 0, 0, "-", "correction"], [30, 0, 0, "-", "registration"]], "sdcflows.workflows.apply.correction": [[29, 1, 1, "", "init_unwarp_wf"]], "sdcflows.workflows.apply.registration": [[30, 1, 1, "", "init_coeff2epi_wf"]], "sdcflows.workflows.base": [[31, 1, 1, "", "init_fmap_preproc_wf"]], "sdcflows.workflows.fit": [[33, 0, 0, "-", "base"], [34, 0, 0, "-", "fieldmap"], [35, 0, 0, "-", "pepolar"], [36, 0, 0, "-", "syn"]], "sdcflows.workflows.fit.base": [[33, 1, 1, "", "init_sdcflows_wf"]], "sdcflows.workflows.fit.fieldmap": [[34, 1, 1, "", "init_fmap_wf"], [34, 1, 1, "", "init_magnitude_wf"], [34, 1, 1, "", "init_phdiff_wf"]], "sdcflows.workflows.fit.pepolar": [[35, 1, 1, "", "init_3dQwarp_wf"], [35, 1, 1, "", "init_topup_wf"]], "sdcflows.workflows.fit.syn": [[36, 1, 1, "", "init_syn_preprocessing_wf"], [36, 1, 1, "", "init_syn_sdc_wf"], [36, 1, 1, "", "match_histogram"]], "sdcflows.workflows.outputs": [[37, 2, 1, "", "DerivativesDataSink"], [37, 1, 1, "", "init_fmap_derivatives_wf"], [37, 1, 1, "", "init_fmap_reports_wf"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "method", "Python method"], "5": ["py", "data", "Python data"], "6": ["py", "exception", "Python exception"], "7": ["py", "property", "Python property"]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:attribute", "4": "py:method", "5": "py:data", "6": "py:exception", "7": "py:property"}, "terms": {"": [5, 7, 10, 11, 12, 14, 15, 17, 18, 23, 29, 34, 35, 36, 37, 39, 41, 42, 44, 45], "0": [5, 7, 10, 12, 13, 14, 15, 18, 19, 20, 22, 25, 29, 34, 35, 36, 39, 41, 42, 44], "0001": [10, 22], "00017": 44, "00059": 18, "001": 5, "00119341": 18, "00246": 20, "00336": 44, "005": 7, "00522": 20, "006": 7, "00746": 7, "00768": 20, "008": 45, "01": [7, 23, 41], "011": 44, "0152472": 44, "01_dir": 7, "01_fieldmap": 7, "01_phase2": 7, "01_phasediff": 7, "01_t1w": 7, "02": 12, "02rad": 12, "03": 44, "04": 41, "05": [23, 41, 44], "05251": 18, "07": [41, 42], "08": [41, 44], "09": 41, "0rc1": 38, "1": [5, 7, 10, 12, 13, 14, 15, 17, 18, 19, 22, 23, 29, 34, 35, 36, 41, 42, 44, 45], "10": [10, 41, 44, 45], "100": [38, 45], "100185": 23, "1002": 44, "1006": 44, "101006": 23, "1016": 44, "102": 38, "10354": 44, "104": 38, "1054": 44, "108": 38, "1099": 44, "11": [5, 41, 44, 45], "1109": 44, "1115": 44, "112254_e9d6d38": 5, "1127": 44, "114": 38, "115": 38, "1156": 44, "116": 38, "1166": 44, "12": [15, 41, 45], "120": 38, "122": 38, "127": [18, 38], "128": 38, "13": [5, 41, 45], "130": 38, "131": 38, "132": 38, "133": 38, "137": 38, "1371": 44, "138": 38, "139": 44, "14": [41, 45], "142": 38, "143": 38, "149": 38, "1492": 44, "15": [5, 41, 45], "150": 38, "151": 38, "152": 38, "153": 38, "154": 38, "155": 38, "156": 38, "157": 38, "159": 38, "16": [5, 10, 39, 41, 42, 44, 45], "160": 38, "161": 38, "162": 38, "164": 38, "165": 38, "166": 38, "168": 38, "17": [10, 44, 45], "170": 38, "171": 44, "172": 38, "173": 38, "174": 38, "175": 38, "176": 38, "178": [38, 44], "18": [41, 45], "180": 38, "182": 38, "184": 38, "185": 38, "188": 38, "19": [44, 45], "190": 38, "191": 38, "1910340111": 44, "193": 44, "197": [38, 44], "199": 38, "1995": 44, "1997": 44, "199706": 44, "1999": 10, "1d": 15, "1ff15ecd54ac": 5, "1mm": 12, "2": [5, 10, 12, 14, 15, 17, 18, 23, 41, 42, 44, 45], "20": [10, 41, 44, 45], "200": [38, 45], "2000": 44, "2001": 44, "2002": 44, "2003": 44, "2004": 44, "2014": 44, "2016": 44, "2017": 44, "2019": 41, "202": 38, "2020": 41, "2021": 41, "2022": 41, "2023": 41, "20231129": 5, "2024": 41, "20241218": 5, "20261": 44, "204": 38, "205": 38, "207": 38, "209": 38, "21": [38, 45], "210": 38, "212": 38, "214": 38, "215": [18, 38], "216": 38, "217": [38, 44], "22": [10, 41, 45], "220451_2d45fdda": 5, "2227266": 18, "223": 38, "224": 38, "228": 38, "229": 38, "23": [5, 41, 45], "230": 38, "234": 38, "237": 38, "239": 38, "24": [5, 41], "240": [38, 44], "243": 38, "247": 38, "248": 38, "25": [5, 41], "251": 38, "253": 38, "254": 38, "257": 38, "258": 38, "26": 41, "261": 38, "262": 38, "263": 38, "265": 38, "269": 38, "27": 41, "270": 38, "276": 38, "277": 38, "278": 38, "28": [12, 34, 38], "280": 38, "281": 38, "282": 38, "284": 38, "285": 38, "287": 38, "288": 38, "29": 41, "292": 38, "293": 38, "298": 38, "299": 38, "2d": 10, "2e6faa0": 38, "2pi": 38, "3": [9, 10, 14, 15, 17, 18, 22, 23, 36, 41, 42, 44, 45], "30": [25, 41], "301": 38, "302": 38, "303": 38, "304": 38, "308": 38, "309": 38, "310": 38, "311": 38, "312": 38, "313": 38, "314": 38, "315": 38, "317": 38, "319": 38, "321": 38, "322": 38, "324": 38, "326": 38, "327": 38, "329": 38, "334": 38, "335": 38, "337": 38, "3389": 44, "339": 38, "34": 44, "3408": 38, "341": 38, "342": 38, "343": 38, "346": 38, "348": 38, "349": 38, "35": 18, "351": 38, "354": 38, "355": 38, "356": 38, "358": 38, "35ff": 5, "36": [5, 23], "360": 38, "361cd67": 38, "364": 38, "366": 38, "367": 38, "368": 38, "371": 38, "374": 38, "375": 38, "379": 38, "38": 10, "380": 38, "381": 38, "387": 38, "39": 38, "390": 38, "391": 38, "393": 38, "394": 38, "396": 38, "398": 38, "399": 38, "3c171": 44, "3d": [10, 14, 44], "3dqwarp": [14, 35, 38, 44], "3e3": 44, "3mm": 36, "3t": 45, "4": [5, 14, 15, 17, 18, 22, 23, 41, 44, 45], "40": 10, "406": 38, "407": 38, "408": 38, "409": 38, "4096": 12, "41": 38, "410": 38, "411": 38, "412": 38, "415": 38, "417": 38, "418": 38, "419": 38, "42": 44, "420": 38, "421": 38, "424": 38, "425": 38, "426": 38, "427": 38, "428": 38, "429": 38, "43": 38, "431": 38, "434": 18, "436": 38, "44": 38, "440": 38, "444": 38, "449": 38, "449c2c2": 38, "45": 38, "450": [38, 44], "452": 38, "453": 38, "457": 38, "458": 38, "459": 38, "460": 38, "461": 44, "462": 38, "463": 38, "463e": 5, "464": 38, "47": 38, "48": [38, 45], "49": [38, 44], "4c2d": 5, "4d": [14, 15, 38], "4mm": 38, "5": [10, 15, 22, 23, 41, 42, 44, 45], "50": [5, 14, 38], "50mm": 12, "51": 38, "51573181152344": 5, "518": 38, "52": [38, 44], "53": 38, "55": 38, "56": 38, "57": 38, "576": 44, "58": 38, "59": 5, "5f": [18, 20], "6": [5, 10, 12, 15, 34, 41, 42, 44, 45], "60": 38, "606491088867188": 5, "61": 38, "62": 5, "63": 38, "65": 44, "7": [5, 13, 25, 41, 44, 45], "70": [38, 45], "717a69": 38, "73": 44, "7325": 18, "75": 38, "79": 38, "7ba673c29221": 5, "8": [5, 25, 39, 41, 45], "80": [38, 45], "8119": 44, "814": 44, "82": 38, "870": 44, "88": 38, "888": 44, "89": 38, "896788": 44, "9": [5, 18, 41, 42, 45], "90": [38, 45], "91": 38, "95": 38, "96": 38, "97": 38, "98": 38, "9f7e": 5, "A": [5, 6, 7, 10, 13, 14, 15, 17, 22, 23, 31, 34, 35, 36, 37, 38, 39, 42, 44], "As": [18, 38, 42], "By": [15, 44], "For": [6, 15, 18, 22, 23, 34, 44, 45], "If": [12, 14, 15, 18, 21, 23, 29, 36, 39, 44], "In": [10, 12, 15, 22, 38, 44, 45], "It": [6, 18, 44], "NOT": 38, "Not": 36, "ONE": 44, "On": [6, 42], "One": [23, 37, 44], "Such": 44, "That": [15, 45], "The": [5, 7, 9, 10, 12, 14, 15, 18, 22, 23, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44], "Then": [18, 44, 45], "There": 44, "These": [10, 23, 42, 44], "To": [14, 23, 38, 44], "With": [10, 18, 38], "_": [10, 17], "__spec__": 6, "__version__": 42, "_bold": 23, "_config": 5, "_dwi": 23, "_fieldmap": [12, 34], "_magnitud": 12, "_magnitude1": 12, "_magnitude2": 12, "_phase1": 12, "_phase2": 12, "_phasediff": 12, "_sbref": 23, "_t1w": 23, "_t2w": 23, "ab": 45, "about": [18, 38], "abov": [10, 34, 42, 45], "absenc": 44, "absolut": [18, 22, 38], "abstract": 13, "abstractcontextmanag": 6, "acc": 18, "acceler": [18, 44], "accept": [6, 22, 38], "access": [5, 6, 38, 41], "accordingli": 38, "account": [10, 18, 22, 44], "accur": [34, 35, 36, 38, 44], "accuraci": 18, "achiev": [15, 38], "acquir": [41, 44, 45], "acquisit": [18, 34, 41, 44], "acr": 6, "across": [5, 15, 35, 36, 38, 45], "action": [5, 38], "actual": [7, 10, 29, 34, 45], "ad": [10, 38], "adapt": [10, 38], "add": [0, 5, 14, 17, 38], "addit": [14, 22, 30, 42, 45], "addition": 38, "address": 38, "addtion": 38, "adebimp": 38, "adopt": 38, "advanc": 38, "affect": 38, "affili": 38, "affin": [6, 10, 12, 15, 38], "afni": [35, 42, 44], "after": [5, 9, 10, 14, 15, 23, 27, 29, 34, 35, 38], "afterward": 38, "aggreg": 39, "aid": [39, 44], "air": [22, 34, 45], "al": [10, 22, 44], "algorithm": [10, 38, 44], "align": [10, 15, 22, 30, 38, 44], "all": [5, 7, 10, 12, 14, 15, 17, 22, 23, 38, 39, 42, 45], "all_index": 45, "all_ndindex": 45, "all_ndindex_warp": 45, "allevi": 10, "alloc": 5, "allow": [5, 18, 23, 38, 39], "allow_neg": 15, "allowed_ent": 37, "along": [10, 18, 29, 38, 44, 45], "alpha": [13, 45], "alreadi": [5, 17, 34, 38, 44], "also": [6, 10, 23, 29, 36, 38, 39, 44], "alter": 38, "altern": [18, 44], "alwai": 10, "ambigu": 38, "amic": 38, "an": [5, 6, 9, 10, 11, 12, 13, 14, 15, 17, 18, 21, 22, 23, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 44, 45], "analys": 39, "analysi": [5, 39, 41, 44], "analysis_level": [0, 5, 39], "anat": [7, 23], "anat_fil": 23, "anat_mask": 36, "anat_nii": 25, "anat_ref": 36, "anat_suffix": 23, "anatom": [5, 23, 30, 34, 36, 37, 38, 44, 45], "anatomi": 45, "anchor": 6, "ancillari": [0, 26], "andersson": 44, "andersson2003": 44, "angl": 45, "ani": [5, 6, 11, 12, 14, 15, 23, 37, 44], "annoi": 38, "anoth": [10, 17], "ant": [5, 12, 14, 15, 30, 38, 39, 42, 44], "anterior": [36, 45], "ants_float": [0, 5], "antsapplytransform": [30, 44], "any_registr": 6, "any_registration_test": 6, "anymor": 10, "anyon": 38, "anyth": 38, "ap": 23, "apach": 38, "api": [38, 41, 44, 45], "app": 38, "appar": 45, "appli": [0, 10, 15, 23, 26, 34, 35, 36, 38, 44], "applic": [41, 44], "apply_mask": 13, "applycoeffsfield": [0, 10, 38], "appreci": 45, "approach": [7, 23, 38, 41], "appropri": [5, 29, 38], "approx": [10, 15, 18], "approxim": [10, 15, 36, 38, 45], "april": 41, "ar": [5, 6, 7, 10, 11, 12, 14, 15, 18, 22, 23, 34, 35, 36, 37, 38, 39, 41, 42, 44, 45], "arang": 45, "arbitrari": [20, 22], "arc": 18, "archiv": 38, "area": 36, "arg": [3, 5, 14, 17], "argument": [5, 7, 14, 23, 38, 41, 44], "argv": 2, "arm64": 38, "around": [18, 22, 25, 38, 45], "arrai": [15, 22, 44, 45], "art": 41, "artifact": [38, 44], "as_fil": 6, "as_path": [0, 6, 41], "asanyarrai": 45, "asl": [23, 38], "asr": 10, "assess": 18, "asset": 10, "assign": 39, "associ": [7, 15, 23, 36, 44], "assum": [12, 36, 44], "astyp": 45, "async": 15, "atla": [36, 38], "atlas_threshold": 36, "attach": 15, "attempt": [15, 23, 44, 45], "attribut": [7, 38], "au2rad": [0, 20], "august": 41, "auto": [25, 38, 45], "auto_": 23, "auto_00000": [17, 23], "auto_00001": [17, 23], "auto_00002": [17, 23], "auto_00003": 23, "auto_00004": 23, "auto_00005": 23, "auto_00006": 23, "auto_00007": 23, "auto_00008": 23, "auto_bold_nss": 36, "autofunct": 6, "autogener": 38, "autom": [5, 7, 44], "automat": [17, 23, 36, 39], "automethod": 6, "avail": [5, 6, 7, 11, 18, 23, 38, 39, 42, 44], "averag": [34, 36, 38, 44], "avoid": [14, 38], "ax": [10, 14, 15, 22, 38, 44, 45], "axcodes2ornt": 22, "axes_grid1": 45, "axi": [10, 14, 15, 44, 45], "axial": [25, 45], "axin": 45, "axis_cbar": 45, "azeez": 38, "b": [10, 15, 17, 22, 23, 27, 29, 34, 35, 36, 38, 44], "b0": [12, 41], "b0field": 38, "b0fieldidentifi": [7, 23, 31, 37, 38, 41], "b0fieldsourc": 38, "b0fieldtransform": [0, 10, 15, 38, 41], "b1": 34, "b_0": [10, 15, 18, 34, 38, 44, 45], "back": [23, 34, 38], "background": 25, "backport": 38, "bad": 38, "baf1": 5, "balaban": 44, "ball": 9, "bandwidth": 45, "base": [0, 5, 7, 9, 10, 11, 12, 13, 14, 15, 17, 26, 32, 34, 35, 36, 37, 41, 42, 44], "base_directori": 37, "base_ent": 23, "basenam": 38, "basi": [15, 38, 44], "basic": [19, 23, 45], "basil": 38, "batteri": 37, "bbox_to_anchor": 45, "bbox_transform": 45, "becaus": [10, 18, 23, 44], "becom": 45, "been": [5, 18, 23, 38, 44], "befor": [5, 15, 38], "beginn": 45, "behavior": 38, "behind": 44, "being": [6, 38, 41], "believ": 18, "below": [36, 44, 45], "berlin": 44, "besid": 34, "best": 10, "bet": 38, "beta": 15, "better": [7, 18, 38], "between": [10, 44], "beyond": 10, "bid": [5, 7, 11, 12, 18, 20, 23, 34, 37, 38, 41], "bidict": [0, 17], "bidirect": 17, "bids_database_dir": [0, 5], "bids_database_wip": [0, 5], "bids_description_hash": [0, 5], "bids_dir": [0, 5, 39], "bids_filt": [0, 5, 23], "bids_fmap_id": 37, "bids_id": [0, 7, 23, 38], "bids_root": [0, 7], "bidsfil": 23, "bidslayout": [5, 23], "bimap": [0, 16], "binari": [9, 14, 34, 42], "binarydil": [0, 9], "biom": 44, "bioscienc": 38, "bit": 18, "black": 45, "blair": 38, "blip": [11, 38], "blob": 39, "blocksiz": 38, "blue": 45, "blur": 15, "bodi": 10, "boilerpl": 38, "bold": [10, 23, 36, 38, 44], "boldref": 38, "bool": [7, 15, 21, 23, 29, 30, 31, 34, 35, 36, 37], "boolean": [10, 12, 13, 14, 37], "border": 15, "bore": 45, "both": [12, 13, 22, 38, 44], "bottom": 45, "bound": [15, 39], "boundari": [7, 10], "brain": [9, 10, 12, 13, 18, 27, 30, 34, 36, 37, 38, 40, 41, 44], "brain_cmap": 45, "brain_mask": [0, 22], "brain_slic": 45, "brainextract": [0, 9], "brainextraction_wf": 27, "brainmask": [0, 8, 27, 36], "branch": 38, "breadcrumb": 21, "break": 38, "bring": 38, "bs_space": 10, "bspline": [0, 8, 38, 44], "bspline_dist": 27, "bspline_grid": [0, 10], "bsplineapprox": [0, 10, 38], "bug": 38, "bugfix": 38, "build": [4, 7, 33, 36, 37, 38, 42, 44], "build_workflow": [0, 4, 5], "built": [5, 23, 44], "bump": 38, "byte": [14, 23], "c": [10, 15, 17, 42, 45], "cach": [0, 5, 6, 15, 38, 39, 41], "caclul": 38, "calcul": [10, 11, 12, 15, 18, 20, 27, 29, 31, 34, 36, 38, 44, 45], "call": [5, 6, 7, 10, 15, 17, 18, 20, 21, 29, 38], "callabl": [6, 15], "can": [5, 7, 10, 14, 15, 18, 22, 23, 30, 34, 39, 42, 44, 45], "candid": [23, 44], "cannot": 17, "capabl": 14, "captur": 38, "cardin": [10, 38], "carri": 15, "case": [6, 10, 12, 23, 30, 38, 44, 45], "cast": 38, "caus": 15, "caution": 44, "cax": 45, "cbar": 45, "cdot": [15, 18, 44], "center": [10, 18, 38, 45], "centerednorm": 45, "central": 38, "chang": [14, 23, 39, 41], "channel": [13, 44], "charact": [7, 38], "character": 44, "cheapli": 38, "check": [3, 5, 12, 14, 38, 42], "check_hdr": 37, "check_path": [0, 7], "checkb0unit": [0, 12], "checkregist": [0, 12], "checksum": 5, "choic": [38, 39], "choke": 38, "choos": [5, 38], "christoph": 38, "ci": 38, "cieslak": 38, "circl": 38, "circleci": 38, "citizen": 38, "class": [0, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 17, 37], "classmethod": 5, "clean": [6, 23], "cleanup": 38, "clear": [0, 17, 38, 44], "clear_registri": [0, 7, 23, 41], "cli": [0, 5, 38, 41], "client": [5, 21], "clip": [27, 44], "close": [15, 45], "cluster": 39, "cmap": 45, "cnr": 38, "co": [36, 44], "code": [5, 10, 14, 29, 30, 34, 35, 36, 38], "codecov": 38, "codespel": 38, "coeff": [0, 15], "coeff2epi": 38, "coeff2epi_wf": [30, 38], "coeffici": [10, 15, 29, 30, 31, 34, 35, 36, 37, 38, 44], "coerc": 37, "cognit": 38, "collat": 38, "collect": [5, 7, 38], "colleg": 38, "collis": 38, "coloc": 38, "color": [25, 45], "colorbar": 45, "colormap": 45, "com": 39, "combin": [15, 31], "come": [23, 45], "command": [2, 3, 5, 14, 41, 42], "comment": 38, "commissur": 45, "commit": 38, "commun": 21, "compact": [15, 44], "compat": [14, 15, 38, 44], "complet": 38, "compliant": [5, 39], "complic": [23, 44], "compon": 44, "comprehens": [23, 38], "compress": [25, 37, 38], "comput": [5, 14, 15, 36], "concaten": 38, "concurr": 38, "conda": 38, "conduc": 38, "config": [0, 38, 39, 41], "config_fil": [4, 5], "configur": [0, 14, 15, 30, 35, 36, 39, 41], "confus": [18, 38], "connect": 38, "consecut": 34, "consid": 38, "consist": [5, 7, 11, 12, 14, 38, 44], "consol": 18, "constant": [15, 45], "constraint": 38, "construct": 38, "consum": 14, "consumpt": 5, "contain": [5, 6, 15, 17, 23, 34, 35, 37, 38, 44], "content": 6, "context": [6, 38], "continu": [5, 38, 44, 45], "contour": 25, "contrast": [6, 36], "contribut": 38, "contributor": 38, "control": [10, 15, 30], "control_zooms_mm": 10, "conveni": 5, "convent": 11, "convers": [5, 35, 36, 38], "convert": [12, 14, 15, 20, 34, 38, 44], "convertwarp": [0, 14], "coolwarm": 25, "coolwarm_transpar": [0, 25], "coordin": [10, 14, 15, 22, 44], "copi": [5, 6, 14, 38, 45], "copy_head": 14, "copyheaderinterfac": 14, "copyright": 38, "core": 34, "coregistr": [38, 44], "cornerston": 44, "coron": 25, "correct": [0, 10, 14, 15, 28, 34, 38, 41, 44], "corrected_mask": 29, "correctli": [23, 38], "correspond": [5, 7, 10, 11, 12, 14, 23, 29, 30, 34, 35, 36, 38, 41, 44, 45], "cosin": [10, 14, 22], "cost": [36, 44, 45], "cover": [22, 38], "coverag": 38, "cox": 44, "cox1997": 44, "cpu": [5, 35, 36, 38, 39], "cpu_count": [0, 5], "crashfil": 5, "crashfile_format": [0, 5], "crawl": 5, "creat": [4, 5, 6, 10, 15, 23, 31, 33, 35, 36, 38], "ctrl_nii": 15, "cubic": [10, 15], "current": [5, 39], "custom": [5, 39], "custom_ent": 37, "cut": 25, "cval": 15, "cwd": [0, 5], "cyceron": 38, "d": [10, 14, 17, 38], "d20231128": 5, "d_": 44, "data": [0, 5, 7, 9, 10, 11, 14, 15, 18, 22, 23, 37, 38, 40, 41], "data2fmap_xfm": 10, "data_dtyp": 37, "databas": [5, 39], "datalad": 38, "dataobj": 45, "dataset": [5, 10, 14, 15, 23, 29, 30, 33, 35, 37, 38, 39, 41], "dataset_descript": 5, "datasink": 37, "datatyp": 37, "date": 38, "deal": [11, 12], "debian": 42, "debug": [0, 5, 10, 29, 30, 31, 34, 35, 36, 38, 39], "debugg": [5, 39], "decemb": 41, "decim": 10, "dedupl": 38, "deep": 38, "def": 45, "default": [0, 5, 9, 10, 12, 13, 14, 15, 25, 27, 31, 34, 37, 38, 39, 44], "defin": [37, 44, 45], "deform": [15, 36, 44], "degre": 15, "del": 17, "delet": 6, "delimit": 39, "delta": [34, 44, 45], "delta_": [18, 20, 44], "delta_t": [0, 20], "demean": [12, 38], "denoiseimag": [0, 14], "dens": 38, "deobliqu": [0, 14, 44], "deoblique_and_zoom": [0, 22], "depart": 38, "depend": [31, 38, 41], "deploi": [38, 42], "deploy": 38, "deprec": 38, "dept": 38, "deriv": [5, 15, 31, 37, 38, 41, 44], "derivativesdatasink": [0, 37, 38], "desc": 45, "describ": [5, 14, 38, 39, 44, 45], "descript": [5, 34, 35, 36, 38, 42], "design": [15, 38, 41, 45], "detach": 38, "detail": [38, 44], "detect": [36, 38], "determin": [10, 15, 22, 29], "dev0": 5, "dev5": 5, "develop": [5, 38, 39, 41, 44], "deviat": 45, "devic": [38, 45], "diagon": 10, "dict": [5, 17, 20, 21, 23, 34, 35, 36, 37], "dictionari": [5, 11, 12, 14, 17, 23, 29, 35, 36, 37], "diff": 12, "differ": [7, 12, 18, 20, 23, 34, 38, 41], "diffus": [23, 44], "dilat": [9, 38], "dimens": [10, 14, 15], "dimension": [14, 44], "dir": [5, 39], "direct": [10, 11, 12, 14, 18, 22, 23, 35, 36, 38, 41], "directli": [6, 10, 15, 34, 38, 44], "director": 10, "directori": [5, 6, 31, 37, 39], "disabl": [5, 7], "disappear": 18, "discov": [38, 41], "discret": 45, "discuss": [18, 44], "disk": 5, "dismiss": [15, 23], "dismiss_ent": 37, "disp_to_fmap": [0, 15, 41], "displac": [12, 14, 15, 29, 36, 38, 44, 45], "displacementsfield2fieldmap": [0, 12], "displai": 41, "distanc": [27, 38], "distinct": 38, "distort": [10, 15, 23, 29, 30, 36, 38, 40, 41], "distortedref": 38, "distribut": [6, 10], "div_id": 25, "divid": [38, 44], "dmriprep": 38, "do": [5, 6, 15, 18, 38, 44], "doc": [5, 38, 39], "docker": [5, 38], "dockerfil": 42, "docstr": [6, 38], "document": [6, 18, 38, 45], "doe": [5, 10, 15, 18, 38], "doi": 44, "done": [18, 34, 38], "dot": [38, 45], "dotsb": [34, 44], "doubl": 38, "download": 38, "downsampl": 38, "downstream": 38, "dr": 18, "drift": 44, "driven": 44, "drop": [5, 15, 38], "dry": [38, 39], "dry_run": [0, 5], "ds000054": 23, "ds000206": 23, "ds001600": 23, "ds001771": [23, 38], "dsa": 23, "dsa_dir": 7, "dsb": 23, "dsc": 23, "dseg": 38, "dtype": [15, 37, 45], "due": 38, "dump": [0, 5, 41], "duplic": 6, "durat": 6, "dure": 38, "dwi": [10, 23, 38, 44], "dynam": 38, "e": [5, 10, 12, 15, 17, 18, 22, 36, 37, 38, 39, 45], "e0152472": 44, "e_i": 45, "e_j": 45, "each": [5, 10, 15, 35, 39, 45], "eafd": 5, "earli": [5, 18], "eas": 44, "easili": [5, 15, 41], "ec": 45, "echo": [18, 34, 38, 41, 44, 45], "echospac": 18, "echotim": [7, 34], "echotime1": [20, 34], "echotime2": [7, 20, 34], "echotimediffer": 20, "edg": 45, "edgecolor": 45, "educ": 45, "ee": 18, "effect": [10, 18, 38, 40, 41, 44], "effectiveechospac": 18, "effici": [6, 38], "effigi": 38, "eilidh": 38, "either": [5, 10, 34], "elaps": 44, "element": [9, 19, 35, 36, 45], "elif": 45, "elsewher": 34, "embed": [10, 15], "emploi": 14, "empric": 38, "empti": [7, 14, 17, 23, 45], "enabl": [5, 7, 10, 31, 38, 39], "encod": [10, 12, 15, 23, 35, 36, 38, 44, 45], "encount": 5, "enforc": 38, "engin": [5, 18], "enh": 38, "enhanc": [38, 44], "enlist": 5, "enough": 18, "ensur": [6, 12, 14, 34, 38], "ensure_positive_cosin": [0, 22], "enter": 6, "enthusiast": 44, "entiti": [0, 7, 23, 37, 38, 39], "entri": 2, "enum": 7, "environ": [0, 5, 14, 41, 42], "epi": [0, 8, 9, 10, 12, 14, 15, 18, 22, 23, 27, 29, 30, 35, 36, 38, 41, 44, 45], "epi_mask": [0, 18, 36], "epi_nii": 15, "epi_ref": 36, "epifactor": 18, "epimanip": [0, 16], "eq": [10, 15, 18, 44], "eqref": [15, 18, 44], "equal": 39, "equival": [18, 34, 44], "error": [5, 7, 10, 18, 38, 44], "especi": [39, 44], "esteban": [38, 44], "esteban2016": 44, "estim": [2, 3, 5, 7, 10, 14, 15, 17, 23, 27, 30, 31, 33, 34, 35, 36, 37, 38, 39, 41, 45], "estimate_bright": 25, "estimatorregistri": [0, 17], "estimatortyp": [0, 7, 23, 41], "et": [10, 44], "etc": [5, 18, 38, 45], "evad": 38, "evalu": [10, 15, 38, 44], "even": [10, 14], "everi": [5, 10, 15, 44], "evid": 12, "exactli": 45, "exagger": 38, "exampl": [5, 7, 17, 19, 20, 23, 41], "except": [5, 7, 23, 39], "exclud": 36, "exclus": [10, 14, 23], "exec_docker_vers": [0, 5], "exec_env": [0, 5], "execut": [0, 2, 3, 4, 5, 14, 15, 23, 36, 39, 41, 44, 45], "exercis": 38, "exist": [5, 6, 9, 10, 11, 12, 13, 14, 37, 39, 44], "exit": [6, 39], "exit_p": 21, "expans": 38, "expect": [6, 12, 14, 36, 38], "experiment": 44, "explicit": [6, 41], "exploit": 44, "export": 5, "expos": 38, "express": [15, 44], "ext": 6, "extend": 15, "extens": 38, "extent": [15, 22, 45], "extern": 41, "extra": [10, 37], "extract": [7, 9, 14, 27, 37, 38], "extrapol": [10, 15, 38], "extrem": [22, 38], "extremelli": 45, "ey": 38, "f": [7, 10, 15, 18, 20, 38], "f_": 18, "fact": 44, "factor": [10, 14, 18, 22, 34, 44], "factor_tol": 22, "fail": 38, "failur": 38, "fairli": 45, "fall": [15, 45], "fals": [5, 6, 7, 10, 12, 13, 14, 15, 23, 25, 29, 30, 31, 34, 35, 36, 37, 39, 45], "fast": [29, 30, 34, 35, 36, 38, 44, 45], "faster": [31, 39], "fastest": 45, "fat": 18, "fc": 45, "featur": 38, "februari": 41, "fed": [11, 35, 44], "feed": 10, "feedback": 44, "few": 23, "fewer": 44, "fiddl": 38, "field": [7, 10, 12, 14, 15, 18, 23, 29, 30, 31, 34, 35, 36, 37, 38, 44], "fieldcoeff": [10, 38], "fieldmap": [0, 2, 3, 5, 10, 11, 12, 13, 15, 17, 20, 23, 27, 29, 30, 31, 32, 35, 36, 37, 38, 39, 41, 45], "fieldmapestim": [0, 7, 17, 23, 31, 38, 41], "fieldmapfil": [0, 7, 23, 38, 41], "fieldmapless": 38, "fieldmapreportlet": [0, 13, 38], "fieldwarp": [29, 38], "fig": [44, 45], "figsiz": 45, "figur": 45, "file": [5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 23, 27, 30, 35, 36, 37, 38, 39, 42], "file1": 17, "file2": 17, "file3": 17, "file4": 17, "file5": 17, "file_path": [0, 5, 41], "filenam": [5, 7, 13, 14, 37, 38], "filepath": 7, "filesystem": [5, 6], "fill": 45, "filter": [5, 10, 15, 23, 38, 39, 44], "final": [15, 23, 38, 41], "find": [10, 18, 23, 38, 39, 44], "find_anatomical_estim": [0, 23], "find_estim": [0, 23, 44], "find_meta": [0, 7], "fine": 38, "first": [5, 10, 14, 18, 35, 36, 38, 44], "fit": [0, 10, 15, 26, 38, 44], "fix": [37, 38, 44], "fixat": 10, "fixed_hdr": 37, "fixup": 38, "flag": [7, 38], "flake8": 38, "flat": 5, "flatten": [0, 14, 17, 35], "fledg": 10, "flexibil": 38, "flexibl": [6, 44], "flexibli": 38, "flirt": 38, "flirtsch": 6, "float": [5, 9, 10, 11, 12, 13, 15, 22, 36, 38], "float32": [15, 45], "float64": 15, "flow": 38, "fm": 23, "fmap": [0, 6, 7, 8, 30, 31, 34, 35, 36, 38], "fmap2data_xfm": 10, "fmap_atla": 6, "fmap_atlas_2_mni152nlin2009casym_affin": 6, "fmap_coeff": [29, 30, 31, 34, 35, 36, 37], "fmap_derivatives_wf": 37, "fmap_fil": 12, "fmap_hz": 15, "fmap_mask": [30, 34, 35, 37], "fmap_nii": 15, "fmap_preproc_wf": 31, "fmap_ref": [10, 30, 31, 34, 35, 36, 37], "fmap_reports_wf": 37, "fmap_target": 10, "fmap_to_disp": [0, 15, 41], "fmap_typ": 37, "fmap_wf": 34, "fmapid": 38, "fmapless": [0, 5, 23, 39, 44], "fmri": 44, "fmriprep": [23, 38], "fninf": 44, "focu": 45, "focus": 38, "folder": [5, 39, 44], "follow": [6, 10, 15, 18, 22, 38, 42, 44], "fontsiz": 45, "footprint": 39, "forc": [5, 14, 23, 39, 44], "force_fmapless": [23, 44], "foreground": [25, 38], "fork": 38, "forkserv": 5, "form": [10, 14, 15, 22, 38], "formal": [10, 15], "format": [5, 15, 29, 44], "formul": [10, 18], "formula": 45, "forward": 38, "found": [18, 23, 38, 39, 42, 44], "four": 23, "fourth": 15, "fov": [12, 38, 45], "frac": [18, 44], "framework": [15, 38, 44], "franc": 38, "free": [5, 19], "free_mem": [0, 5, 29], "freedom": 15, "freeli": 44, "freesurf": [5, 42], "freie": 44, "frequenc": [18, 38], "from": [5, 6, 7, 10, 11, 12, 14, 15, 18, 19, 20, 22, 23, 27, 29, 34, 36, 37, 38, 39, 42, 44, 45], "from_dict": [0, 5, 41], "from_fil": [9, 10, 11, 12, 14], "front": [0, 19, 38, 44], "fsl": [10, 11, 18, 34, 35, 38, 42, 44], "full": [6, 15, 25], "fulldataset": 15, "fulli": [6, 10, 22], "func": [6, 15], "function": [0, 5, 6, 15, 22, 23, 36, 38, 42, 44], "fund": 39, "furo": 38, "further": [3, 18, 44], "furtherr": 45, "fuse": 45, "g": [5, 10, 12, 18, 36, 37, 38, 39, 45], "gaa86b0b08f": 5, "gamma": [18, 44], "gaussian": 14, "gb": [5, 39], "gener": [6, 10, 12, 13, 15, 17, 22, 30, 31, 34, 38, 45], "geometr": 44, "get": [0, 5, 17, 18, 38, 41, 45], "get_cent": 45, "get_data": 38, "get_fdata": [38, 45], "get_free_mem": [0, 19], "get_identifi": [0, 7, 41], "get_kei": [0, 17], "get_linked_lib": [0, 5], "get_plugin": [0, 5], "get_trt": [0, 18], "get_workflow": [0, 7], "getlogg": [0, 5], "getreadouttim": [0, 11], "getter": 6, "gh": 38, "gha": 38, "git": 38, "github": [38, 39], "given": [5, 7, 12, 15, 20, 23, 27, 29, 35, 36, 38, 39, 44, 45], "goncalv": 38, "gone": 10, "gorgolewski": 38, "govern": 45, "gradient": 44, "grai": 45, "graph": [4, 5, 29, 30, 34, 35, 36, 38], "grappa": 18, "grayscal": [18, 22, 45], "gre": [9, 27, 34, 44], "greater": [6, 39], "grid": [10, 15, 22, 29, 35, 38, 45], "grid_bspline_weight": [0, 10, 15, 41], "grid_refer": 35, "ground": 45, "group": [22, 38, 39], "gt": 15, "guid": [18, 34], "guidelin": 38, "gyromagnet": [18, 44], "gz": [6, 7, 12, 18, 34, 45], "h": [38, 39, 44], "ha": [5, 10, 15, 18, 22, 23, 38, 44, 45], "habitu": 42, "had": 38, "handl": [15, 38, 41, 42], "happen": [5, 15, 45], "hard": [5, 38], "harvard": 38, "hashmap": 17, "have": [5, 10, 12, 14, 15, 22, 23, 25, 34, 35, 36, 38, 44, 45], "hcp": [23, 38], "hcp101006": 23, "hcph": 5, "head": [10, 15, 29], "header": [10, 14, 37, 38], "hear": 38, "height": 45, "held": 18, "help": [39, 45], "henc": 10, "here": [10, 15, 18, 22, 44], "heurist": [5, 23, 38, 44], "hi": 18, "high": [38, 44], "higher": [38, 44], "histogram": [36, 44], "histori": 38, "hmc": [10, 15], "hmc_xfm": 15, "hmc_xform": 29, "home": [5, 39], "homogen": 38, "horizont": 45, "hospit": 38, "host": 38, "hot": 38, "hotfix": 38, "housekeep": 38, "how": [15, 18, 23, 42, 44, 45], "howev": [39, 45], "hpc": 39, "http": 39, "human": 5, "huntenburg": 44, "huntenburg2014": 44, "hutton": 44, "hutton2002": 44, "hz": [12, 13, 15, 20, 29, 34, 37, 38, 44], "i": [5, 6, 7, 10, 11, 12, 14, 15, 17, 18, 21, 22, 23, 25, 30, 34, 36, 38, 39, 41, 42, 44], "id": 5, "idea": 38, "ident": [22, 38], "identifi": [5, 7, 15, 23, 38, 39, 44], "ieee": [10, 44], "ignor": 38, "ij": 45, "im": 45, "imag": [10, 11, 12, 14, 15, 18, 22, 23, 27, 29, 30, 34, 36, 38, 41, 45], "imagingfrequ": 18, "img": [10, 18, 22], "img_mask": 36, "immedi": 38, "impact": 38, "implement": [5, 6, 10, 15, 18, 38, 41], "implicit": 41, "import": [5, 6, 22, 23, 38, 42, 45], "importlib": 6, "importlib_resourc": 6, "impos": 45, "improv": [6, 38, 39], "imshow": 45, "in1": 9, "in2": 9, "in_": 31, "in_anat": 36, "in_coeff": 10, "in_data": [10, 11, 14, 35], "in_epi": [14, 36], "in_field": 14, "in_fil": [9, 11, 12, 14, 18, 20, 22, 27, 37], "in_mask": [10, 14], "in_meta": [12, 14, 18, 20, 36], "in_orient": 14, "in_phas": [12, 20], "in_plumb": 14, "in_refer": 22, "in_valu": 20, "in_xfm": 10, "includ": [6, 15, 23, 38, 39, 44], "inclus": 23, "incomplet": 38, "inconsist": 38, "incorpor": 38, "incorrect": 38, "increas": [22, 38, 39], "incub": 38, "inde": 45, "independ": [15, 39], "index": [5, 7, 14, 15, 35, 39, 45], "indic": [5, 7, 14, 23, 39], "indicate_inset_zoom": 45, "individu": [29, 30, 31, 34, 44], "induc": 38, "infer": [7, 14], "inform": [0, 5, 38, 39, 44], "infrastructur": 38, "inhomogen": [29, 44], "init": [0, 5, 21], "init_3dqwarp_wf": [0, 35], "init_brainextraction_wf": [0, 27], "init_coeff2epi_wf": [0, 30], "init_fmap_derivatives_wf": [0, 37], "init_fmap_preproc_wf": [0, 31, 38], "init_fmap_reports_wf": [0, 37], "init_fmap_wf": [0, 34], "init_magnitude_wf": [0, 34], "init_p": 21, "init_phdiff_wf": [0, 34], "init_sdcflows_wf": [0, 33], "init_syn_preprocessing_wf": [0, 36, 38, 44], "init_syn_sdc_wf": [0, 36, 44], "init_topup_wf": [0, 35, 38], "init_unwarp_wf": [0, 29], "initi": [5, 7, 21, 23, 38], "inlin": [38, 45], "inlist": 19, "input": [5, 7, 9, 10, 11, 12, 13, 14, 15, 20, 22, 23, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 44], "input_imag": 14, "insert": [17, 38, 45], "inset": 45, "inset_ax": 45, "inset_loc": 45, "insid": 45, "inspect": 12, "instal": [5, 38, 41], "instanc": [7, 22, 23, 38, 39, 44], "instead": [15, 38], "instrument": 41, "int": [15, 22, 27, 29, 30, 31, 34, 35, 36, 45], "inted": 38, "integ": [10, 14, 27, 44], "integr": [38, 44], "intend": [6, 14], "intendedfor": [7, 23, 38, 41], "intens": [36, 38, 44], "intensityclip": 38, "intent": [38, 44], "interact": 38, "interfac": [5, 6, 7, 22, 38, 39, 41, 44], "intermedi": [5, 39], "intern": [15, 35, 36, 38], "interpol": [10, 15, 29, 38, 44], "interpret": [6, 42, 44], "intersphinx": 38, "intramodalmerg": 38, "introduc": [15, 38, 44], "inu": 38, "invers": [15, 22, 36], "invert": [22, 38], "investig": 23, "is_in_fov": 45, "ishandl": 38, "isol": 38, "issu": [5, 38, 45], "item": [10, 11, 12, 14, 17, 37], "iter": 15, "itertool": 45, "itk": [12, 14, 15, 29, 30], "itk_format": 15, "itk_transform": 12, "its": [10, 29, 34, 37, 44], "j": [10, 11, 12, 14, 15, 18, 22, 38, 44], "j_axi": 45, "jacobian": [10, 15, 29, 38], "januari": 41, "jenkinson": 44, "jenkinson2003": [34, 44], "jezzard": 44, "jezzard1995": 44, "job": 39, "join": 5, "joinpath": 6, "journal": 44, "json": [5, 6, 7, 18, 39], "juli": 41, "june": 41, "jupyt": 38, "just": [5, 10, 15, 27, 34], "k": [10, 11, 12, 14, 15, 22, 44, 45], "k_1": 15, "k_2": 15, "k_3": 15, "keep": [5, 38], "kei": [11, 12, 14, 17, 23, 37, 38], "kernel": [5, 15, 38], "kevin": 38, "keyerror": 17, "keyserv": 38, "keyword": 7, "king": 38, "knot": 15, "known": [10, 18], "krzysztof": 38, "kwarg": [7, 13, 17, 21], "l": 44, "la": 22, "label": [13, 15, 18, 23, 25, 31, 38, 39, 44], "labelbottom": 45, "labelleft": 45, "laplacian": 44, "larg": [14, 38, 39], "larger": 45, "last": [0, 7, 17, 18, 19, 20, 38], "latest": 38, "latex": 38, "latter": 30, "lausann": 38, "layout": [0, 5, 23, 39], "least": 44, "left": [5, 18, 37, 38, 45], "legaci": [38, 44], "legal": 10, "len": 45, "length": 18, "less": [5, 23, 31, 34, 35, 36, 38, 39, 41], "lessen": 14, "let": [44, 45], "level": [5, 6, 15, 23, 38, 39, 44], "leverag": 38, "lfloor": 18, "librari": [5, 41], "licens": [5, 42], "lifespan": 38, "lifetim": 6, "lighten": 15, "like": [5, 6, 15, 36, 38, 39], "likewis": 23, "limit": [5, 10, 38, 39, 45], "line": [2, 3, 5, 14, 41, 42], "linear": [15, 44], "linewidth": 45, "link": [5, 18, 38, 44], "linux": 5, "list": [5, 7, 10, 11, 12, 14, 15, 17, 19, 23, 29, 31, 34, 35, 36, 37, 39], "listserv": 18, "liter": 38, "literatur": 44, "load": [0, 5, 6, 38, 41, 45], "load_data": 6, "loader": [0, 6, 38, 41], "loc": 45, "local": [5, 38], "local_hash_check": [0, 5], "locat": [10, 15, 37, 44, 45], "log": [0, 38, 39, 41], "log_dir": [0, 5], "log_level": [0, 5], "logger": [0, 5, 23, 41], "london": 38, "look": [5, 36], "lookup": 38, "loop": 15, "loosen": 38, "lower": [23, 45], "lowest": 45, "lp": 22, "lr_epi": 7, "lsqr": 38, "lw": 45, "m": [10, 42, 44], "m0scan": 23, "machin": 38, "macnicol": 38, "mag_fil": 12, "magazin": 10, "magic": 5, "magn": 44, "magnet": 18, "magneticfieldstrength": 18, "magnitud": [10, 12, 27, 30, 34, 37, 38, 44], "magnitude1": [23, 38], "magnitude2": [23, 38], "magnitude_wf": 34, "mai": [6, 7, 10, 12, 15, 18, 29, 30, 31, 34, 39, 41, 44], "main": [0, 1, 38, 45], "maint": 38, "maintain": 5, "mainten": 38, "major": [38, 44], "make": [14, 38, 42, 44], "makefil": 38, "manag": [5, 6], "mandatori": [9, 10, 11, 12, 13, 14, 23, 37], "mani": [23, 44], "manifest": 38, "manipul": [18, 20, 38], "manual": 23, "manuscript": 38, "map": [0, 10, 12, 14, 15, 17, 20, 23, 27, 29, 30, 34, 36, 37, 38, 41], "map_coordin": 45, "march": 41, "mark": 10, "markiewicz": 38, "marku": 38, "mask": [9, 10, 13, 14, 18, 22, 27, 29, 30, 34, 35, 36, 37, 38], "mask_anat": 36, "mass": 38, "massag": [34, 38], "master": [39, 44], "mat": 6, "match": [7, 10, 36, 37], "match_histogram": [0, 36], "materi": 45, "mathbf": [10, 15], "mathia": 38, "matplotlib": 45, "matric": [10, 15, 29, 38], "matrix": [15, 18, 38], "matt": 44, "matter": 18, "matthew": 38, "max": 45, "max_alpha": [13, 25], "max_concurr": 15, "max_tr": 14, "maximum": [13, 15, 29, 30, 31, 34, 38, 39], "maxtasksperchild": 5, "mean": [5, 10, 12, 23, 39, 44, 45], "measur": [34, 45], "mechan": 18, "med": 44, "median": 10, "medicin": 38, "mem": 39, "memori": [5, 15, 19, 38, 39], "memory_gb": [0, 5, 39], "merg": [36, 38], "meshgrid": 45, "messag": [23, 38], "meta": 18, "meta_dict": 37, "metadata": [0, 7, 11, 12, 14, 15, 18, 20, 23, 29, 34, 35, 36, 37, 38, 44], "metadataerror": [0, 7, 41], "method": [0, 6, 7, 15, 23, 34, 35, 36, 38, 41], "metric": 36, "mgr": 5, "mhz": 18, "middl": [25, 45], "miga": 21, "migrat": 38, "mika\u00ebl": 38, "min": 45, "miniconda": 38, "minim": [5, 38, 39, 41], "minimum": [10, 38], "minor": 38, "mirror": 15, "misc": [0, 16], "miscellan": 19, "misconfigur": 38, "miss": [23, 38], "mixin": 13, "mktemp": 5, "mm": [12, 36], "mni": 36, "mni152nlin2009casym": [5, 38, 45], "mnt": 38, "mock": 38, "mode": [5, 10, 15, 29, 30, 34, 35, 36, 38, 39, 44], "model": [14, 44, 45], "modifi": [10, 25, 38], "modul": [0, 1, 6, 8, 16, 24, 26, 28, 32, 38, 41], "moduletyp": 6, "monitor": 5, "more": [10, 12, 23, 34, 36, 37, 38, 44], "morpholog": [18, 22], "mosaic": 13, "most": [5, 7, 15, 17, 18, 20, 22, 38, 44], "motion": [10, 15, 29], "move": [10, 13, 15, 30, 38], "moving_label": 13, "mp2rage": 45, "mpl": 45, "mpl_toolkit": 45, "mprage": [10, 45], "mr": [41, 44], "mri": [34, 39, 41, 44], "mri_robust_regist": 12, "mrm": 44, "much": 45, "multi": [15, 23, 33, 38, 39, 44], "multipl": [6, 35, 38, 39, 44], "multiplex": 38, "multiproc": 5, "multiprocess": 5, "multithread": 5, "multivers": 38, "must": [5, 15, 23, 35, 42], "mutual": [10, 14, 44], "n": [6, 14, 15, 38, 39, 44], "n4": [27, 34, 38], "n_": 18, "n_proc": 38, "name": [5, 6, 7, 13, 18, 23, 27, 29, 30, 31, 34, 35, 36, 37, 38, 41], "namespac": 3, "nan": [38, 45], "natur": 22, "naveau": 38, "nb": 45, "nbm453": 44, "ndarrai": 15, "ndi": 45, "ndimag": 45, "nearest": 15, "necessari": [6, 14, 18, 23, 34, 38, 44], "need": [5, 34, 38, 45], "neg": 15, "neighbor": 44, "neither": 18, "neurodock": 42, "neuroimag": [38, 41, 42, 44], "neuroinform": 44, "neurostar": 18, "new": [5, 10, 17, 22, 41], "newest": 38, "newli": 38, "newpath": 20, "next": 38, "nibabel": [15, 22, 45], "nibabi": 38, "nice": 38, "niflow": 38, "nifti": [10, 14, 15, 23, 37, 44], "nifti1imag": [10, 15], "nii": [6, 7, 12, 18, 34, 45], "nimg": 44, "niprep": [38, 39, 41], "nipyp": [0, 4, 5, 9, 10, 12, 13, 14, 37, 38, 39, 41, 42], "nipype1": 38, "nipype_vers": [0, 5], "nitranform": 38, "niworkflow": 38, "nmr": 44, "node": 38, "nois": [10, 14, 34], "noise_imag": 14, "noise_model": 14, "noisi": 38, "nomin": [38, 45], "non": [38, 44], "nonbrain": 27, "none": [2, 3, 5, 7, 9, 10, 11, 12, 14, 15, 17, 18, 20, 21, 22, 23, 25, 29, 36, 37, 39, 44, 45], "nonlinear": 44, "nonneg": 15, "nonstandard": 18, "nonsteadi": 36, "nonuniform": 34, "nonzero": 44, "norm": 45, "normal": [38, 44, 45], "note": 18, "notebook": [38, 45], "noth": 7, "notic": 38, "notrack": [0, 5, 39], "novemb": 41, "now": [19, 38], "np": 45, "nproc": [0, 5, 39], "nthread": 39, "num_thread": [10, 14, 15], "number": [5, 10, 14, 15, 18, 22, 29, 30, 31, 34, 35, 36, 38, 39, 44, 45], "numpi": [15, 37, 38, 45], "nutshel": [40, 41, 44], "o": [5, 14, 15, 34, 37, 38, 44], "obj": [15, 34], "object": [5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 23, 37, 38, 45], "obliqu": [10, 14, 22, 38, 44], "obtain": [10, 18, 22, 39, 44], "occurr": 39, "octob": 41, "odd": [10, 38], "oe": 18, "oesteban": 5, "off": 38, "offer": 41, "offset": 44, "old": 38, "omp": 39, "omp_nthread": [0, 5, 29, 30, 31, 34, 35, 36, 39], "onc": 18, "one": [10, 12, 15, 22, 23, 34, 38, 44], "ones_lik": 45, "onli": [5, 14, 15, 22, 23, 38, 39, 44, 45], "onto": [10, 15, 44], "opaque_perc": 25, "open": [39, 41], "openneuro": 23, "openpgp": 38, "oper": [5, 6, 15, 18, 22, 38, 39], "oppos": [35, 45], "opt": [5, 39], "optim": [10, 38, 44], "option": [5, 9, 10, 11, 12, 13, 14, 15, 18, 23, 27, 31, 35, 36, 37, 38, 41, 44], "oracl": 38, "orchestr": 38, "order": [15, 22, 25, 38], "org": 38, "orient": [10, 22, 38, 45], "origin": [5, 10, 14, 15, 37, 38, 45], "ornt_transform": 22, "orthogon": 35, "oscar": 38, "osf": 38, "oslo": 38, "other": [0, 10, 15, 22, 23, 38, 41, 42], "other_packag": 6, "otherwis": [19, 38], "our": [15, 23, 38, 45], "out": [5, 15, 37, 38, 39], "out_": 31, "out_brain": 27, "out_coeff": 10, "out_correct": 10, "out_data": [11, 14], "out_epi": 14, "out_error": 10, "out_extrapol": 10, "out_field": [10, 14], "out_fil": [9, 12, 14, 18, 22, 27, 37], "out_intercept": 10, "out_list": 14, "out_mask": [9, 14, 27], "out_meta": [14, 37], "out_path_bas": 37, "out_probseg": [9, 27], "out_report": 13, "out_warp": [36, 38], "outcom": 44, "outlier": 38, "output": [0, 5, 9, 10, 11, 12, 13, 14, 15, 26, 27, 29, 30, 31, 34, 35, 36, 38, 39, 44], "output_dir": [0, 5, 31, 37, 39], "output_dtyp": 15, "output_imag": 14, "outputnod": 38, "outsid": [10, 13, 15, 38], "over": [6, 15, 18, 38], "overcommit": 5, "overcommit_limit": [0, 5], "overcommit_polici": [0, 5], "overestim": 38, "overflow": 15, "overhaul": 38, "overlai": 25, "overlay_param": 25, "overli": 38, "overload": 37, "overrid": [15, 38], "overwrit": 7, "p": [5, 10, 44], "pa": [23, 38], "pacifi": 38, "packag": [0, 38, 41, 42], "pad": [14, 22, 38], "padslic": [0, 14], "page": 38, "pair": [12, 17, 23, 34, 38], "pandoc": 38, "parallel": [5, 15, 18, 35, 36, 39, 44], "parallelreductionfactorinplan": 18, "param": 45, "paramet": [5, 7, 12, 14, 15, 18, 22, 23, 27, 29, 30, 31, 34, 35, 36, 37, 38, 44], "parekh": 18, "pars": 3, "parse_arg": [0, 3], "parser": [0, 1], "part": [34, 38, 41], "partial": 38, "particip": [5, 23, 31, 39], "participant_id": 5, "participant_label": [0, 5, 39], "particular": [5, 17, 34, 45], "particularli": 38, "pass": [5, 6, 12, 22, 23, 38, 44], "patch": [10, 38], "path": [0, 5, 6, 7, 10, 15, 19, 34, 35, 36, 37, 38, 39, 42], "pathlik": [9, 10, 11, 12, 13, 14, 15, 34, 37], "pdb": [0, 5, 39], "pdf": [29, 30, 34, 35, 36], "pe": [11, 18, 29, 35, 36, 44], "pe_dir": [10, 11, 12, 14, 15, 22], "pe_dir_fsl": 11, "pe_direct": 11, "pe_dirs_fsl": 11, "pe_info": 15, "pennsylvania": 38, "pep517": 38, "pepolar": [0, 10, 23, 30, 32, 38, 41], "pepolar4p": 23, "pepolar_estimate_wf": 35, "per": [15, 18, 23, 34, 38], "perelman": 38, "perfect": 10, "perform": [7, 22, 30, 38, 41, 44], "permiss": 38, "perturb": 45, "phase": [10, 12, 15, 20, 23, 34, 35, 36, 38, 41, 45], "phase1": [12, 34, 38], "phase2": [12, 34], "phase_diff": 12, "phasediff": [10, 12, 23, 34, 38, 44], "phasediff2fieldmap": [0, 12], "phaseencodingdirect": [15, 18, 22, 23], "phasemanip": [0, 16], "phasemap2rad": [0, 12], "phdiff2fmap": [0, 20], "phdiff_wf": 34, "phenomenon": [40, 41], "philip": 18, "phyisic": 45, "physic": [15, 40, 41, 44], "pi": [34, 44], "pick": [14, 23], "pickl": 5, "pictur": 45, "piec": 38, "piecewis": 15, "pin": 38, "ping": 21, "pinsard": 38, "pip": 42, "pipelin": [38, 44], "pixel": [10, 18], "pkg_resourc": 38, "pkgdata": 6, "place": 23, "plan": 5, "planar": [41, 44, 45], "plane": 18, "platform": [5, 41], "plausibli": 44, "pleas": [18, 38], "plo": 44, "plot": [25, 38, 45], "plot_brain": 45, "plot_param": 25, "plot_registr": [0, 25], "plt": 45, "plugin": [0, 5, 39], "plugin_arg": [0, 5], "plumb": [10, 14, 38], "png": [29, 30, 34, 35, 36], "point": [2, 10, 15, 38, 44], "polar": [14, 22, 38, 44], "poldrack": 38, "polici": 5, "pone": 44, "pop": 19, "popul": 38, "posit": [10, 14, 22, 41, 44], "positivedirectioncosin": [0, 14], "posix": 5, "posixpath": 5, "possibl": [5, 6, 18, 23, 39, 44], "post": 18, "posterior": 36, "postprocess": 38, "potenti": [14, 38], "ppm": 18, "pr": 38, "pravesh": 18, "pre": [41, 44], "precis": [5, 31], "precomput": 22, "precondit": 10, "prefer": 18, "prefilt": [15, 22], "prefix": [5, 39], "prelud": 34, "prepar": [21, 34, 36, 38, 44], "prepopul": 39, "preprocess": [5, 18, 31, 34, 36, 37, 38, 41, 44], "present": [23, 38], "prevent": 38, "previou": [15, 38, 44], "previous": [5, 38, 39], "principl": 10, "print": 42, "prior": 38, "priorit": 38, "prioriti": 23, "probabilist": 9, "probabl": 27, "probe": 19, "problem": [10, 18, 38, 44, 45], "procedur": 44, "process": [5, 10, 22, 29, 30, 31, 34, 39, 41, 44], "processor": 39, "produc": [30, 38, 44, 45], "product": [10, 15, 22, 38, 45], "program": [6, 14, 38, 39, 41], "progress": 10, "project": [10, 22, 44], "promin": [38, 44], "propag": [15, 37], "properti": [17, 22], "proport": 44, "propos": 44, "protocol": [38, 41, 44], "proton": 44, "provid": [6, 7, 15, 18, 23, 34, 38, 39, 41, 44], "psi": [10, 15], "psl": 22, "psychologi": 38, "pull": 38, "purpos": [23, 30, 44], "push": 38, "put": 38, "pybid": [5, 23, 38, 39], "pypi": 42, "pyplot": 45, "python": [5, 6, 21, 38, 39, 41, 42], "q": [10, 45], "qualifi": 6, "qualiti": 30, "qualnam": 7, "quantit": 44, "queri": [23, 38], "quick": [18, 22], "quit": 18, "quiver": 45, "r": [38, 44, 45], "ra": [10, 15, 22, 38], "rad": [7, 12, 20, 38], "radian": [12, 44], "radiologi": 38, "radiu": [9, 12], "rais": 18, "raise_insuffici": 5, "ram": 5, "random": [27, 38], "rang": [12, 15, 34, 38, 44], "rather": [10, 15, 38, 44], "ratio": [18, 44], "rcparam": 45, "rdpu_r": 45, "re": [5, 38, 39], "reach": 27, "read": [5, 6, 7, 20], "read_text": 6, "readabl": [0, 6, 41], "readout": [10, 11, 12, 15, 18, 29, 44], "readout_tim": 11, "real": 39, "realign": 15, "realiti": 45, "realli": 38, "reason": [10, 38], "reced": 10, "receiv": [7, 44], "recent": [7, 10, 17, 18, 20, 34], "reconstruct": [10, 15, 18, 44], "reddish": 45, "reduc": 45, "ref_mask": 36, "refacor": 38, "refactor": 38, "refer": [10, 13, 14, 15, 22, 23, 27, 29, 30, 31, 34, 35, 36, 37, 38, 41, 45], "reference_label": 13, "reflect": 15, "refresh": 38, "regard": [5, 18], "region": [34, 36, 44, 45], "regist": [12, 15, 38], "registr": [0, 12, 13, 15, 28, 36, 38, 39, 41], "registri": [7, 23, 38], "regress": 12, "regular": [10, 15, 36, 45], "rel": [6, 38, 42], "relai": 23, "relat": [38, 41], "relax": 38, "releas": 41, "relev": 38, "reli": 34, "reliabl": 38, "remain": 6, "remot": 38, "remov": [5, 10, 15, 27, 34, 38, 39], "remove_node_directori": [0, 5], "renam": 38, "render": 38, "reobliqu": [0, 14], "reorient": [14, 22, 38], "reorient_pedir": [0, 22], "reorientimageandmetadata": [0, 14], "repeat": 17, "replac": [7, 27, 38], "repo": 38, "report": [5, 13, 18, 37, 38], "reportcapableinterfac": 13, "reportlet": [0, 8, 38], "repres": [5, 7, 9, 10, 11, 12, 13, 14, 15, 37, 44], "represent": [5, 15, 38, 44], "reproduc": 41, "request": [6, 22, 38], "requir": [6, 21, 34, 38, 41, 42], "rerun": 38, "resampl": [10, 14, 15, 22, 30, 36, 38], "resample_to_zoom": [0, 22], "research": 44, "reshap": 45, "resolut": [22, 38, 45], "resolv": [10, 38], "reson": 44, "resort": 44, "resourc": [5, 6, 38], "resource_monitor": [0, 5, 9, 10, 11, 12, 14], "respect": 22, "respons": [0, 41], "restor": 5, "restore_env": [0, 5, 41], "restrict": [36, 38], "result": [5, 6, 10, 15, 38, 39, 44, 45], "retain": 10, "retouch": 38, "return": [7, 15, 17, 19, 22, 23, 38, 45], "retval": [4, 5], "reus": [15, 38], "revers": [15, 17, 18, 44], "review": 18, "revis": [10, 38], "rf": 38, "rfloor": 18, "rician": 14, "ridge_alpha": 10, "right": [18, 19, 37], "rigid": 10, "ro": [18, 44], "ro_tim": [10, 12, 15], "robust": [38, 41, 44], "robustaverag": 38, "rodent": 38, "roll": 38, "root": [5, 7, 10, 38, 39], "rootlogg": 5, "rorden": 18, "ross": 38, "rot_thresh": 12, "rotat": [10, 12, 22, 38, 44], "rotim": 18, "round": 45, "run": [3, 5, 12, 14, 23, 29, 30, 34, 35, 36, 38, 39], "run_unique_id": 5, "run_uuid": [0, 5], "runner": [5, 38, 39], "runtim": 5, "russel": 38, "s1053": 44, "s_": [44, 45], "s_1": 15, "s_2": 15, "s_3": 15, "sagitt": 25, "same": [6, 10, 12, 14, 15, 38, 39, 44], "sampl": [10, 15, 22], "sampled_field": 45, "samples_i": 45, "samples_x": 45, "sanit": [7, 38], "sanitized_id": [0, 7, 38], "sar": 10, "satterthwait": 38, "save": [14, 31, 37, 38], "save_nois": 14, "sbref": [23, 38], "scalar": 14, "scale": [25, 29, 34, 38, 45], "scale_unit": 45, "scan": [15, 18, 41, 44, 45], "scanner": [38, 44, 45], "scatter": 45, "scheme": [41, 44, 45], "school": 38, "scipi": [38, 45], "scm": 38, "scope": 6, "scrutin": 44, "sd": [36, 44, 45], "sd_prior": 36, "sd_syn": 6, "sd_syn_sloppi": 6, "sdc": [10, 15, 23, 27, 31, 38, 44], "sdcflow": [0, 39, 42, 44, 45], "search": [7, 23, 44], "second": [10, 15, 18, 36, 44], "secret": 38, "section": [0, 15, 41, 44], "see": [5, 15, 23, 38, 44, 45], "seed": 38, "seem": 18, "seen": 45, "segfault": [10, 14], "segment": [6, 44], "sei": [38, 44], "seismic": 45, "select": [38, 45], "self": [17, 38], "semaphor": 15, "send": [21, 39], "send_crumb": [0, 21], "sens": 18, "sensit": 38, "separ": [6, 27, 34, 38], "septemb": 41, "sequenc": [15, 34, 41], "seri": [15, 41], "serv": 37, "server": 21, "session": [5, 23, 38, 39, 44], "session_label": [0, 5, 39], "set": [5, 10, 15, 18, 23, 29, 36, 37, 38, 39, 42, 44], "set_aspect": 45, "set_input": 7, "set_ticklabel": 45, "set_xlim": 45, "set_xticklabel": 45, "set_ylim": 45, "set_yticklabel": 45, "setup": [21, 38], "setup_miga": [0, 21], "setuptool": 38, "setuptools_scm": 38, "sever": [38, 39, 44], "sha256": 5, "shape": [10, 12, 15, 38, 45], "share": [5, 38, 39], "shift": [12, 15, 18, 44], "shim": [38, 44], "short": [34, 35, 36], "shortest": 38, "should": [5, 7, 12, 13, 14, 15, 18, 22, 23, 34, 35, 36, 37, 38, 39, 44, 45], "show": [13, 38, 39], "shown": 13, "shrink": 14, "shrink_factor": 14, "sici": 44, "sidecar": [7, 18], "siemens2rad": 38, "sign": 15, "signal": [10, 38, 45], "significantli": 12, "similar": 38, "similarli": 23, "simpl": 38, "simplebeforeaft": 38, "simpleinterfac": [9, 10, 11, 12, 14], "simpli": 6, "simplic": 44, "simplifi": [23, 38], "simplist": 38, "simultan": 39, "singl": [5, 14, 15, 23, 31, 38, 39, 44], "singleton": 5, "sitek": 38, "size": [18, 29], "sjshim": 38, "sk": 38, "skim": 38, "skip": 23, "skull": [30, 34, 36, 44], "slice": [14, 38, 44, 45], "slightli": [15, 45], "sloppi": [0, 5, 29, 30, 31, 34, 35, 36, 38, 39], "small": 38, "smaller": 38, "smart": 27, "smeisler": 38, "smooth": [10, 44], "smriprep": 38, "sneve": 38, "so": [6, 10, 11, 12, 36, 38, 44, 45], "soft": 27, "softwar": [38, 42, 44], "solver": 38, "some": [5, 6, 7, 18, 23, 27, 34, 38, 42, 44, 45], "somewher": 19, "sort": [7, 11, 27, 38], "sortpeblip": [0, 11], "sourc": [0, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 25, 27, 29, 30, 31, 33, 34, 35, 36, 37, 41, 44], "source_fil": 37, "source_ornt": 22, "space": [10, 15, 18, 29, 30, 36, 37, 38, 39, 44, 45], "spars": 15, "spatial": [10, 14, 15], "spatialimag": [15, 22, 38], "speci": [0, 5], "special": [7, 13, 17, 38], "specif": [0, 7, 38, 41, 45], "specifi": [14, 36, 38], "speech": 38, "spgr": 45, "sphinx": 38, "spike": 10, "spin": 44, "spinoza": 18, "spiral": 38, "spline": [10, 15, 27, 29, 34, 35, 36, 38, 44], "split": 38, "spread": 44, "sqlite": 5, "squeez": 38, "sra": 10, "stabil": 38, "stabl": 38, "stack": 14, "stage": [10, 44], "standalon": [2, 3, 4, 38, 41], "standard": [14, 18, 38, 39], "stanford": 38, "start": [5, 7, 38, 45], "stat": 38, "state": [36, 41], "statement": 18, "std2anat_xfm": 36, "step": [10, 15, 44, 45], "stop": [5, 38], "stop_on_first_crash": [0, 5], "store": [5, 18, 37, 39, 44], "str": [5, 6, 7, 14, 15, 23, 27, 29, 30, 31, 34, 35, 36, 37], "strang": 18, "strategi": [7, 10, 15, 31, 38, 44], "strength": [18, 45], "string": [5, 9, 10, 11, 12, 13, 14, 23, 37], "strip": [30, 34, 36, 44], "strong": 36, "structur": [5, 9, 15, 23, 38, 44], "studholm": 44, "studholme2000": 44, "studi": 44, "style": 30, "sub": [5, 7, 39, 45], "subject": [5, 23, 31, 33, 38], "submit": [12, 38], "submodul": [0, 38, 41, 44], "suboptim": 5, "subordin": 38, "subpackag": [0, 41], "subplot": 45, "subprocess": 5, "subsequ": [34, 44], "subtract": [34, 38], "subtract_phas": [0, 20], "subtractphas": [0, 12], "successfulli": 23, "suffer": 44, "suffici": [38, 45], "suffix": [0, 5, 7, 23, 38, 39, 45], "suit": [38, 44], "sum_": 15, "summar": 18, "summari": 44, "sunja": 38, "support": [4, 15, 34, 35, 36, 38], "sure": [38, 42], "surfac": 44, "surround": 34, "suscept": [15, 23, 36, 38, 40, 41, 44], "svg": [13, 29, 30, 34, 35, 36], "svgutil": 38, "swapax": 45, "switch": [5, 38], "symmetr": 44, "symmetri": 44, "syn": [0, 10, 14, 32, 38, 44], "syn_preprocessing_wf": 36, "syn_sdc_wf": 36, "system": [14, 22, 39, 42], "t": [10, 15, 18, 20, 44, 45], "t1": 41, "t1w": [7, 23, 36, 38, 44, 45], "t1w_invers": 36, "t2": [36, 45], "t2w": [36, 38, 44], "t_": [18, 44], "t_mask": 36, "tabl": [7, 38], "tag": [15, 18, 38, 44], "take": [34, 35, 44], "taken": 35, "target": [5, 10, 15, 22, 29, 30, 37, 38, 44], "target2fmap_xfm": [30, 38], "target_affin": 15, "target_mask": 30, "target_nii": 15, "target_orient": 14, "target_ornt": 22, "target_ref": 30, "target_refer": 15, "task": [5, 35, 36], "te": [20, 34, 44], "techniqu": 41, "technologi": 38, "telemetri": [0, 16], "templat": [5, 36], "template_id": [0, 5], "templateflow": [5, 45], "templateflow_hom": [0, 5], "templateflow_vers": [0, 5], "temporari": [6, 15], "tensor": [10, 15, 38, 44], "tesla": 44, "test": [5, 23, 38], "test_wrangler_uri": 38, "texliv": 38, "text": [5, 18, 20, 34, 44], "than": [10, 38], "thank": 38, "thei": [11, 38, 44], "them": 12, "themselv": 38, "theodor": 38, "theoret": 38, "theori": 41, "therefor": [10, 15, 22, 35, 44], "thereof": 30, "thesi": 44, "theta": 44, "theta_i": 44, "thi": [5, 6, 7, 10, 12, 14, 15, 18, 21, 22, 23, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 44], "think": 45, "third": 17, "thorough": 18, "those": [10, 44, 45], "thread": [5, 10, 14, 29, 30, 31, 34, 38, 39], "three": 44, "threshold": [12, 36], "through": [6, 10, 12, 14, 15, 38], "throughout": 6, "thu": 22, "tick": 45, "time": [5, 6, 10, 11, 12, 14, 15, 18, 29, 38, 39, 44], "timepoint": [10, 36], "tissu": [27, 45], "tmp": 5, "to_displac": [0, 15], "to_filenam": [0, 5, 41], "togeth": [36, 38], "toggl": 38, "toler": [22, 38], "toml": 5, "tool": [0, 5, 15, 16, 25, 38, 41, 42, 45], "top": [6, 39, 45], "topup": [10, 11, 14, 35, 38, 44], "topupcoeffreori": [0, 10], "total": [5, 11, 12, 15, 18, 44], "total_memori": [0, 5], "totalreadouttim": [7, 18], "toward": [38, 45], "tr": 14, "trace": 30, "traceback": [7, 17, 18, 20], "track": [5, 17, 39], "train": 18, "tran": 44, "trans_thresh": 12, "transax": 45, "transform": [0, 10, 12, 22, 30, 36, 41, 44], "transformcoeffici": [0, 10], "transit": 38, "translat": 12, "translation_rigid": 6, "transpar": [25, 38], "transparent_perc": 25, "travers": 6, "travisci": 38, "treat": [6, 14], "treatment": 38, "treiber": 44, "treiber2016": 44, "tri": 14, "trigger": [38, 39], "trivial": 10, "trt": 45, "true": [5, 6, 7, 10, 12, 14, 15, 17, 21, 22, 23, 29, 36, 37, 39, 44, 45], "truth": 45, "try": 44, "tune": 38, "tupl": [7, 10, 14, 15, 19, 34, 36, 45], "turn": 45, "two": [12, 18, 20, 22, 23, 34, 35, 38, 39, 44, 45], "txt": [5, 17], "type": [7, 11, 12, 15, 17, 23, 37, 44], "typeerror": 17, "typic": [6, 15, 41, 44], "typo": 38, "u": [12, 20, 45], "ubuntu": 38, "ucbn": 38, "um": 38, "un": 38, "unavil": 38, "uncompress": 37, "under": [5, 38, 39], "underscor": 7, "understand": 45, "undistort": 10, "uneven": 14, "unhash": 17, "uniform": [38, 44], "uniformgrid": [0, 14], "union": [0, 9], "uniqu": [5, 7, 29, 30, 34], "unit": [7, 12, 15, 20, 29, 34, 37, 38], "unittest": 38, "univers": 38, "universit\u00e4t": 44, "unknown": [5, 39], "unless": [15, 38], "unmodifi": 37, "unpack": 6, "unsaf": 38, "unsanit": 38, "unser": 10, "unser1999": [10, 15], "unsupport": 41, "untouch": 19, "unus": 38, "unwarp": [10, 15, 29, 35, 36, 38, 41], "unwarp_parallel": [0, 15, 41], "unwarp_wf": [29, 38], "unwrap": [34, 38, 44], "up": [5, 6, 29, 36, 37, 38, 42, 44], "updat": [10, 12, 15, 22, 38, 44], "upgrad": 38, "upload": 38, "upper": [15, 39], "upstream": 38, "uri": 38, "url": 38, "us": [5, 6, 7, 10, 12, 14, 15, 18, 22, 23, 29, 30, 31, 34, 36, 38, 39, 42, 44], "usa": 38, "usabl": 38, "usag": [0, 6, 41], "use_plugin": 39, "user": [5, 23, 34, 38, 41], "util": [0, 5, 7, 8, 15, 24, 38, 41, 44], "ux": 38, "v": [14, 39, 44, 45], "v1": 38, "val": 17, "valid": [7, 15, 18, 23, 38, 39], "valu": [5, 7, 9, 10, 11, 12, 13, 14, 15, 17, 23, 37, 38, 45], "valueerror": [7, 17, 18, 20, 38], "variabl": [5, 14], "variat": 44, "variou": [11, 12], "vector": 45, "vein": 38, "veloc": 44, "vendor": 18, "ventricl": 45, "verbos": [5, 14, 38, 39], "veri": [23, 45], "verifi": 12, "version": [0, 5, 7, 14, 38, 39, 42], "via": [5, 44], "view": [25, 38, 45], "virtual": 5, "vision": 38, "visual": [13, 25, 38, 44, 45], "viz": [0, 41], "vmax": 45, "vmin": 45, "volum": [15, 35, 36, 38, 45], "voxel": [10, 15, 22, 27, 29, 36, 44, 45], "voxel_centers_c": 45, "voyag": 18, "vsm": [15, 38, 44], "vvv": 39, "w": [18, 38, 39], "wa": [14, 15, 34, 35, 36, 37, 38], "wai": 38, "walker": 27, "wang": 44, "wang2017": 44, "want": [7, 15, 39, 44], "warn": [5, 38], "warp": [14, 36, 44, 45], "warped_brain": 45, "warped_edg": 45, "water": 18, "waterfatshift": 18, "we": [7, 10, 12, 15, 23, 34, 38, 44, 45], "weekli": 38, "weight": [15, 38, 41], "well": [10, 38, 44], "were": [38, 44], "wf": 18, "what": [39, 41], "when": [5, 6, 7, 10, 15, 23, 34, 38, 39, 44, 45], "whenev": [5, 38], "where": [5, 6, 10, 12, 13, 15, 18, 36, 39, 44, 45], "whether": [5, 12, 22, 29, 34, 35, 36, 37, 45], "which": [5, 7, 10, 11, 12, 14, 15, 18, 31, 35, 37, 38, 39, 44, 45], "while": 38, "white": 45, "whole": 4, "whose": [5, 22], "why": 10, "wide": [5, 33], "width": 45, "wipe": [5, 39], "wire": 38, "within": [10, 18, 38, 39, 44, 45], "without": [10, 12, 14, 36, 38], "wm": 38, "wonder": 18, "word": [10, 15, 22], "work": [5, 38, 39, 45], "work_dir": [0, 5, 39], "workabl": 44, "workdir": 38, "worker": [0, 15, 41], "workflow": [0, 1, 5, 7, 23, 38, 41, 44], "world": 39, "would": [6, 45], "wrangler": [0, 16, 38, 44], "wrap": [6, 12, 14, 15, 34, 44], "write": [5, 37, 38], "write_coeff": [30, 37], "write_graph": [0, 5], "written": [5, 37, 42], "wrong": [18, 38], "x": [10, 11, 14, 25, 41], "x1": 45, "x2": 45, "x_coord": 45, "xfm": [15, 22], "xfm_data2fmap": 15, "xtick": 45, "xxxxx": 39, "xy": 45, "xyz_nii": 15, "y": [10, 11, 14, 25, 38], "y1": 45, "y2": 45, "y_coord": 45, "y_coord_mov": 45, "yield": [6, 44], "you": 39, "your": [15, 42, 45], "ytick": 45, "z": [10, 11, 14, 25, 38], "z_": 45, "z_slice": 45, "zaitsev": 44, "zaitsev2004": 44, "zero": [10, 13, 23, 38, 45], "zip": [6, 45], "zoom": [10, 22, 38, 44], "zooms_min": 10}, "titles": ["Library API (application program interface)", "sdcflows.cli package", "sdcflows.cli.main module", "sdcflows.cli.parser module", "sdcflows.cli.workflow module", "sdcflows.config module", "sdcflows.data package", "sdcflows.fieldmaps module", "sdcflows.interfaces package", "sdcflows.interfaces.brainmask module", "sdcflows.interfaces.bspline module", "sdcflows.interfaces.epi module", "sdcflows.interfaces.fmap module", "sdcflows.interfaces.reportlets module", "sdcflows.interfaces.utils module", "sdcflows.transform module", "sdcflows.utils package", "sdcflows.utils.bimap module", "sdcflows.utils.epimanip module", "sdcflows.utils.misc module", "sdcflows.utils.phasemanip module", "sdcflows.utils.telemetry module", "sdcflows.utils.tools module", "sdcflows.utils.wrangler module", "sdcflows.viz package", "sdcflows.viz.utils module", "sdcflows.workflows package", "sdcflows.workflows.ancillary module", "sdcflows.workflows.apply package", "sdcflows.workflows.apply.correction module", "sdcflows.workflows.apply.registration module", "sdcflows.workflows.base module", "sdcflows.workflows.fit package", "sdcflows.workflows.fit.base module", "sdcflows.workflows.fit.fieldmap module", "sdcflows.workflows.fit.pepolar module", "sdcflows.workflows.fit.syn module", "sdcflows.workflows.outputs module", "What\u2019s new?", "Standalone command line usage", "Examples", "SDCFlows", "Installation", "&lt;no title&gt;", "Methods and implementation", "Susceptibility Distortions in a nutshell"], "titleterms": {"": 38, "0": [38, 45], "01": 38, "04": 38, "05": 38, "07": 38, "08": 38, "09": 38, "1": 38, "10": 38, "11": 38, "12": 38, "13": 38, "14": 38, "15": 38, "16": 38, "18": 38, "2": 38, "20": 38, "2019": 38, "2020": 38, "2021": 38, "2022": 38, "2023": 38, "2024": 38, "22": 38, "23": 38, "24": 38, "25": 38, "26": 38, "27": 38, "29": 38, "3": 38, "30": 38, "4": 38, "5": 38, "6": 38, "7": 38, "8": 38, "9": 38, "The": 45, "absolut": 45, "acquisit": 45, "also": 18, "ancillari": 27, "api": 0, "appli": [28, 29, 30], "applic": 0, "approach": 44, "april": 38, "argument": 39, "august": 38, "author": 38, "b0": 44, "b0fieldidentifi": 44, "b_": 45, "base": [31, 33, 38], "bid": [39, 44], "bimap": 17, "blip": 45, "brain": 45, "brainmask": 9, "bspline": 10, "chang": 38, "cli": [1, 2, 3, 4], "cocktail": 45, "command": 39, "config": 5, "configur": 5, "content": [40, 41], "correct": 29, "data": [6, 44, 45], "dataset": 44, "decemb": 38, "depend": 42, "differ": 44, "direct": [44, 45], "discov": 44, "distort": [44, 45], "effect": 45, "epi": 11, "epimanip": 18, "estim": 44, "exampl": 40, "explicit": 44, "extern": 42, "februari": 38, "field": 45, "fieldmap": [7, 34, 44], "fit": [32, 33, 34, 35, 36], "fmap": 12, "handl": 39, "i": 45, "imag": 44, "implement": 44, "implicit": 44, "ingredi": 45, "instal": 42, "instrument": 39, "intendedfor": 44, "interfac": [0, 8, 9, 10, 11, 12, 13, 14], "januari": 38, "juli": 38, "june": 38, "less": 44, "librari": 0, "line": 39, "list": 38, "log": 5, "mai": 38, "main": 2, "map": 44, "march": 38, "method": 44, "misc": 19, "modul": [2, 3, 4, 5, 7, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 25, 27, 29, 30, 31, 33, 34, 35, 36, 37], "mri": 45, "name": 39, "neg": 45, "new": 38, "novemb": 38, "nutshel": 45, "octob": 38, "off": 45, "option": 39, "other": [5, 44], "output": 37, "packag": [1, 6, 8, 16, 24, 26, 28, 32], "paper": 38, "parser": 3, "pe": 45, "pepolar": [35, 44], "perform": 39, "phase": 44, "phasemanip": 20, "phenomenon": 45, "physic": 45, "posit": 39, "pre": 38, "program": 0, "refer": 44, "registr": [30, 44], "relat": 39, "releas": 38, "reportlet": 13, "respons": 5, "revers": 45, "sampl": 45, "sdcflow": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41], "second": 45, "section": 5, "see": 18, "septemb": 38, "sequenc": 44, "seri": 38, "specif": 44, "standalon": 39, "submodul": [1, 8, 16, 24, 26, 28, 32], "subpackag": 26, "suscept": 45, "syn": 36, "t1": 44, "techniqu": 44, "telemetri": 21, "text": 45, "thank": 18, "theori": 44, "thi": 45, "tool": [22, 44], "trade": 45, "transform": 15, "uniform": 45, "unsupport": 44, "unwarp": 44, "usag": [5, 39], "util": [14, 16, 17, 18, 19, 20, 21, 22, 23, 25], "viz": [24, 25], "weight": 44, "what": 38, "workflow": [4, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37], "wrangler": 23, "x": 38}})
\ No newline at end of file