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sMRIPrep 0.13 #376

Merged
merged 143 commits into from
Nov 20, 2023
Merged

sMRIPrep 0.13 #376

merged 143 commits into from
Nov 20, 2023

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effigies
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Omnibus PR merging the next branch into master.

TODO:

@effigies
RF: Split surface workflow into recon and derivative preparation
8e8eea9
@effigies
MNT: Update .gitignore
9dfa265
@effigies
RF: Break derivatives worfklow into first and second derivatives
9b9a5ce
@effigies
RF: Split workflows.norm into workflows.fit.registration and workflow…
fe60be3 
…s.apply.resampling
@effigies
RF: Use split workflows in anat_preproc_wf
de8e62b
@effigies
RF: Factor out brainmask refinement workflow
5f152d9
@effigies
RF: Reorganize anat into fit and derivatives
58b8a3a 
Currently skipping report generation and LiterateWorkflow descriptions
@effigies
FIX: Continue on missing fast-track items
37aade1
@effigies
RF: Deprecate --fast-track for --derivatives
54bbc2e
@effigies
ENH: Add logging during workflow build
27a4d97
@effigies
WRAPPER: Patch in derivatives
5d2b755
@effigies
RF: Use pre-computed template warps
73eb03f
@effigies
RF: Split first derivatives workflow
5b07196 
Overall the goal is to have buffers full of non-workflow paths.

Compute -> sink -> list for downstream use
@effigies
ENH: Use ITK transforms in FreeSurfer contexts
890fc3e
@effigies
FIX: Workflow connections
d47338b
@effigies
RF: Drop unused predict_derivatives function
7429106
@effigies
RF: Skip fsnative registration if transform is found
c1f022e
@effigies
STY: Unused import
3123fbd
@effigies
DOC: Add precomputed arg to workflow, remove old output
ee28819
@effigies
FIX: Add fit_wf.inputnode explicitly
dca427e
@effigies
MNT: Re-add workflow description
dc5eb34
@effigies
Add types to workflow parameters
4f6369c
@effigies
DOC: Restore docstring for anat_fit_wf, update argument ordering
e12ee79
@effigies
DOC: Update output docs, make a note of organization
52c7994
@effigies
FIX: Drop t1w_realign_xfm from outputnodes
257a5c8
@effigies
DOC: Update anat_preproc_wf arguments and docs
ada61ac
@effigies
STY: black
a31959d
@effigies
FIX: Un-split badly split f-string
cf96ab5
@effigies
RF: Re-attach report workflow
b4ae477
@effigies
DOC: Fix docstring
b1f4c5c
effigies and others added 26 commits November 9, 2023 12:42
@effigies
Merge pull request #383 from effigies/fix/msm-invert-sulc
c238409 
FIX: Invert sulcal depth metric before passing to MSM, use HCP atlas files
@effigies
Merge remote-tracking branch 'upstream/master' into next
619b157
@effigies
Merge remote-tracking branch 'upstream/master' into next
55605ec
@effigies
FIX: Missing JSON brace
cfc0592
@effigies
MNT: Refine pre-commit exclusions
c7e9c1d
@effigies
STY: Apply pre-commit
b5e8663
@effigies
ENH: Annotate mris_expand with thread usage
43eed0e
@effigies
Update smriprep/interfaces/freesurfer.py
899f2f4
@effigies
MNT: Remove AFNI from smriprep docker container
de41f41
@effigies
Merge pull request #387 from effigies/docker/drop-afni
1c00cee 
MNT: Remove AFNI from smriprep docker container
@effigies
Merge pull request #386 from effigies/enh/multithread-mrisexpand
6ce2121 
ENH: Annotate mris_expand with thread usage
@effigies
RF: Generalize InvertShape to MetricMath
dfc26ff
@effigies
RF: Move InvertSulc to MetricMath, update imports
76edb42
@effigies
ENH: Add workflow to convert HCP-style morphometry GIFTIs
58276c0
@effigies
ENH: Add workflow to resample GIFTIs to fsLR and generate CIFTIs
d9f1bff
@effigies
RF: Add template-space datasink workflow, iterate in main workflow
22fd48d
@effigies
RF: Add CIFTI morphometrics datasink workflow
36029c0
@effigies
FIX: std2anat -> anat2std_xfm in ds_std_volumes_wf connection
808889b
@effigies
FIX: Only create CIFTI workflows if cifti_output is set
7c5802f
@effigies
DOC: Checkpoint SpatialReferences in docstring workflows
373c8ed
@effigies
DOC: Add omp_nthreads to init_morph_grayords_wf() docstring
25a9769
@effigies
FIX: hcp_morphometrics_wf connection
5edd05f
@effigies
RF: Separate midthickness resampling from morphometry resampling
a08d9cf
@effigies
ENH: Reconnect datasinks
afa5620
@effigies
FIX: Fetch MSM registration from correct buffer
0bf46d1
@effigies
Merge pull request #388 from effigies/rf/template-resampling-workflows
3c2edb7 
RF: Split template and fsLR resampling and sinking into isolated workflows
effigies
effigies commented Nov 19, 2023
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@effigies effigies merged commit d7bda97 into master Nov 20, 2023
23 of 24 checks passed
@effigies effigies deleted the next branch November 20, 2023 00:47
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@effigies