Merge pull request #12 from mrfil/qsiprep-v0.15.1

docs/source/Install.rst

@@ -13,7 +13,6 @@ To get started with the pipeline, please install the following requirements:
     * Brain Connectivity Toolbox for Matlab (https://sites.google.com/site/bctnet/Home/functions/BCT.zip?attredirects=0) 
     * xcpEngine dsn files (https://github.com/PennBBL/xcpEngine/tree/master/designs) 
     * ASHS (https://sites.google.com/site/hipposubfields/) 
-    * LAYNII (https://github.com/layerfMRI/LAYNII) 
     * bidsphysio (https://github.com/cbinyu/bidsphysio)
 
 You will need to install git, to clone the build recipe files from this repository.
@@ -31,17 +30,14 @@ This following commands can be used to build these required images for the pipel
 
     singularity build mriqc-0.16.1.sif docker://poldracklab/mriqc:0.16.1
     singularity build heudiconv-0.9.sif docker://nipy/heudiconv:0.9.0
-    singularity build fmriprep-v20.2.6.sif docker://nipreps/fmriprep:21.0.0
-    singularity build xcpengine-1.2.3.sif docker://pennbbl/xcpengine:1.2.3
-    singularity build qsiprep-v0.14.3.sif docker://pennbbl/qsiprep:0.14.3
-    #for reorient_fslstd to prepare for SCFSL_GPU
-    singularity build qsiprep-v0.14.3.sif docker://pennbbl/qsiprep:0.15.1
+    singularity build fmriprep-v21.0.1.sif docker://nipreps/fmriprep:21.0.1
+    singularity build xcpengine-1.2.4.sif docker://pennbbl/xcpengine:1.2.4
+    singularity build qsiprep-v0.15.1.sif docker://pennbbl/qsiprep:0.15.1
 
     # See README.md for more information on 
     # provided def files for ubuntu-jq, python3
-    SINGULARITY_NOHTTPS=1 singularity build ubuntu-jq-0.1.sif defjq
+    SINGULARITY_NOHTTPS=1 singularity build ubuntu-jqjo.sif jqjo.def
     SINGULARITY_NOHTTPS=1 singularity build python3.sif defpy3
-    SINGULARITY_NOHTTPS=1 singularity build laynii-2.0.0.sif layniidef
     SINGULARITY_NOHTTPS=1 singularity build ashs-1.0.0.sif ashsdef
 
     #Start Docker registry for localhost

docs/source/Sub-Pipelines.rst

@@ -110,11 +110,11 @@ Using the structural images and fieldmaps, we perform diffusion-weighted-image p
 
 .. code-block:: bash
 
-    docker run -v ${IMAGEDIR}:/imgdir -v ${stmpdir}:/paulscratch -v ${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives /data/bids/ --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+    docker run -v ${IMAGEDIR}:/imgdir -v ${stmpdir}:/paulscratch -v ${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives /data/bids/ --freesurfer-input /data/bids/derivatives/fmriprep/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
 
 .. code-block:: bash
 
-    singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+    singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --freesurfer-input /data/bids/derivatives/fmriprep/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
 
 *Reconstruction*
 
@@ -123,15 +123,15 @@ Constrained Spherical Deconvolution-based multi-shell multi-tissue w/ SIFT2 via
 .. code-block:: bash
 
     #run reconstruction workflow in QSIPrep
-    docker run -v ${IMAGEDIR}:/imgdir -v ${stmpdir}:/paulscratch -v ${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec mrtrix_multishell_msmt --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+    docker run -v ${IMAGEDIR}:/imgdir -v ${stmpdir}:/paulscratch -v ${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec mrtrix_multishell_msmt_ACT-hsvs --freesurfer-input /data/bids/derivatives/fmriprep/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
     
     #calculate network-based statistics and save NxN matrices from .net
     docker run -v ${scripts}/matlab:/work -v ${scripts}/2019_03_03_BCT:/bctoolbox -v ${projDir}/bids/derivatives/qsirecon:/data ${IMAGEDIR}/matlab-R2019a.sif /work/qsinbs.sh "$subject" "$sesname"
 
 .. code-block:: bash
 
     #run reconstruction workflow in QSIPrep
-    singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec mrtrix_multishell_msmt --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+    singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec mrtrix_multishell_msmt_ACT-hsvs --freesurfer-input /data/bids/derivatives/fmriprep/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
     
     #calculate network-based statistics and save NxN matrices from .net
     singularity run --cleanenv --bind ${scripts}/matlab:/work,${scripts}/2019_03_03_BCT:/bctoolbox,${projDir}/bids/derivatives/qsirecon:/data ${IMAGEDIR}/matlab-R2019a.sif /work/qsinbs.sh "$subject" "$sesname"
@@ -141,7 +141,7 @@ Generalized q-Sampling imaging via DSI Studio
 .. code-block:: bash
 
     #run reconstruction workflow in QSIPrep
-    docker run -v ${IMAGEDIR}:/imgdir -v ${stmpdir}:/paulscratch -v ${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec dsi_studio_gqi --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+    docker run -v ${IMAGEDIR}:/imgdir -v ${stmpdir}:/paulscratch -v ${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec dsi_studio_gqi --freesurfer-input /data/bids/derivatives/fmriprep/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
 
     #get network-based statistics to a csv from .mat
     docker run -v ${scripts}:/scripts -v ${projDir}/bids/derivatives/qsirecon/${subject}/${sesname}/dwi:/datain -W /datain ${IMAGEDIR}/pylearn.sif /scripts/gqimetrics.py
@@ -150,7 +150,7 @@ Generalized q-Sampling imaging via DSI Studio
 .. code-block:: bash
 
     #run reconstruction workflow in QSIPrep
-    singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec dsi_studio_gqi --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+    singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec dsi_studio_gqi --freesurfer-input /data/bids/derivatives/fmriprep/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
 
     #get network-based statistics to a csv from .mat
     singularity run --cleanenv --bind ${scripts}:/scripts,${projDir}/bids/derivatives/qsirecon/${subject}/${sesname}/dwi:/datain -W /datain ${IMAGEDIR}/pylearn.sif /scripts/gqimetrics.py
@@ -160,15 +160,15 @@ NODDI via AMICO python implementation
 .. code-block:: bash
 
     #run reconstruction workflow in QSIPrep
-    docker run -v ${IMAGEDIR}:/imgdir -v ${stmpdir}:/paulscratch -v ${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec amico_noddi --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+    docker run -v ${IMAGEDIR}:/imgdir -v ${stmpdir}:/paulscratch -v ${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec amico_noddi --freesurfer-input /data/bids/derivatives/fmriprep/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
 
     #ROI-wise stats       
     docker run -v ${scripts}:/scripts -v ${projDir}/bids/derivatives/qsirecon/${subject}/${sesname}/dwi:/datanoddi ${IMAGEDIR}/neurodoc.sif /scripts/noddi_stats.sh "$subject" "$sesname"
 
 .. code-block:: bash
 
     #run reconstruction workflow in QSIPrep
-    singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec amico_noddi --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+    singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.14.3.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec amico_noddi --freesurfer-input /data/bids/derivatives/fmriprep/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
 
     #ROI-wise stats       
     singularity run --cleanenv --bind ${scripts}:/scripts,${projDir}/bids/derivatives/qsirecon/${subject}/${sesname}/dwi:/datanoddi ${IMAGEDIR}/neurodoc.sif /scripts/noddi_stats.sh "$subject" "$sesname"
@@ -187,12 +187,12 @@ QSIPrep preprocessing reorient to FSL space:
 .. code-block:: bash
 
     #run reconstruction workflow in QSIPrep
-    docker run -v ${IMAGEDIR}:/imgdir -v ${stmpdir}:/paulscratch -v ${projDir}:/data ${IMAGEDIR}/qsiprep-v0.15.1.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec reorient_fslstd --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+    docker run -v ${IMAGEDIR}:/imgdir -v ${stmpdir}:/paulscratch -v ${projDir}:/data ${IMAGEDIR}/qsiprep-v0.15.1.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec reorient_fslstd --freesurfer-input /data/bids/derivatives/fmriprep/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
 
 .. code-block:: bash
 
     #run reconstruction workflow in QSIPrep
-    singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.15.1.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec reorient_fslstd --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+    singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.15.1.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec reorient_fslstd --freesurfer-input /data/bids/derivatives/fmriprep/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
 
 
 CUDA 10.2-accelerated FDT pipeline

docs/source/Usage.rst

@@ -44,6 +44,7 @@ Running FreeSurfer-informed FSL DTI tractography on GPU
 *Docker*
 
 .. code-block:: bash
+
     # Running SCFSL GPU tractography
     docker exec --gpus all -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-10.2/lib64 \
     -v /path/to/freesurfer/license.txt:/opt/freesurfer/license.txt \
@@ -52,6 +53,7 @@ Running FreeSurfer-informed FSL DTI tractography on GPU
 *Singularity*
 
 .. code-block:: bash
+
     # Running SCFSL GPU tractography
     SINGULARITY_ENVLD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-10.2/lib64 \
     singularity exec --nv -B /path/to/freesurfer/license.txt:/opt/freesurfer/license.txt,/path/project/bids:/data \

docs/source/conf.py

@@ -21,7 +21,7 @@
 author = 'Paul B Camacho, Evan D Anderson, Nishant Bhamidipati, Aaron T Anderson, Benjamin Zimmerman, Matthew S Moore, Ezra Paul Winter-Nelson, Maximillian K Egan, Brad P Sutton'
 
 # The full version, including alpha/beta/rc tags
-release = '0.1.0'
+release = '0.3.0'
 
 
 # -- General configuration ---------------------------------------------------
@@ -53,4 +53,4 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
-pygments_style = 'sphinx'
+pygments_style = 'sphinx'

jsoncrawler.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 #
 #single-sub single-session script for adding intended for statements to fmap jsons before running BIDS apps
-#
+# requires JQ
 #usage: jsoncrawler.sh {bids directory} {session} {subject}
 #
 #pbc
@@ -10,7 +10,6 @@
 sesname=$2
 seslen=${#sesname}
 sub=$3
-intend='"IntendedFor": '
 
 seshs=($1/${sub}/${sesname})
 for sesh in ${seshs[@]}; do
@@ -20,21 +19,15 @@ restfuncs=(./func/*rest*bold*nii.gz)
 
 	for restfuncmap in ${restfuncmaps[@]}; do
 	img=${restfuncs:1}
-	jq .IntendedFor $restfuncmap > tmpj
+	jq '.IntendedFor' $restfuncmap > tmpj
 	if [[ $(cat tmpj) == "${sesname}${img}" ]];
 	then
 		echo "IntendedFor found as "${sesname}$img""
 		exit 0
 	else
-		printf "  " > test.txt
-		printf $intend >> test.txt
-		printf " " >> test.txt
-		printf '"' >> test.txt
-		printf "${sesname}""$img"  >> test.txt
-		printf '",' >> test.txt
-		echo "" >> test.txt
-		echo "" > tmp
-		awk 'NR==1{a=$0}NR==FNR{next}FNR==32{print a}1' test.txt $restfuncmap >> tmp && mv tmp $restfuncmap
+		# replace the following with jq or jo 
+		cat $restfuncmap | jq '.IntendedFor |= "${sesname}$img"' > tmp
+		mv tmp $restfuncmap
 	fi
 done
 
@@ -48,22 +41,8 @@ taskfuncs=`find ./func -maxdepth 2 -type f \( -iname "*nback*bold*nii.gz" -a -no
 	task="*nback*"
 	if [[ "$img" == "$task" ]];
 	then
-#		jq .IntendedFor $taskfuncmap > tmpj
-#		if [[ "`cat tmpj`" == "${sesname}$img" ]];
-#		then
-#			echo "IntendedFor found as "${sesname}$img""
-#			exit 0
-#		else
-			printf "  " > test.txt
-	       	printf $intend >> test.txt
-        	printf " " >> test.txt
-        	printf '"' >> test.txt
-        	printf "${sesname}""$img"  >> test.txt
-        	printf '",' >> test.txt
-        	echo "" >> test.txt
-        	echo "" > tmp
-        	awk 'NR==1{a=$0}NR==FNR{next}FNR==32{print a}1' test.txt $taskfuncmap >> tmp && mv tmp $taskfuncmap     
-
+		cat $taskfuncmap | jq '.IntendedFor |= "${sesname}$img"' > tmp
+		mv tmp $taskfuncmap
 	fi
 done
 
@@ -72,25 +51,16 @@ dwis=(./dwi/*dwi*nii.gz)
 
 	for dwimap in ${dwimaps[@]}; do
 	img=${dwis:1}
-		jq .IntendedFor $dwimap > tmpj
+		jq '.IntendedFor' $dwimap > tmpj
 		if [[ $(cat tmpj) == "${sesname}$img" ]];
 		then
 			echo "IntendedFor found as "${sesname}$img""
 			exit 0
 		else
-			printf "  " > test.txt
-        	printf $intend >> test.txt
-        	printf " " >> test.txt
-        	printf '"' >> test.txt
-        	printf "${sesname}""$img"  >> test.txt
-        	printf '",' >> test.txt
-        	echo "" >> test.txt
-        	echo "" > tmp
-        	awk 'NR==1{a=$0}NR==FNR{next}FNR==32{print a}1' test.txt $dwimap >> tmp && mv tmp $dwimap
+			cat $dwimap | jq '.IntendedFor |= "${sesname}$img"' > tmp
+            mv tmp $dwimap
 		fi
 done
 done
 
-rm -f test.txt
-rm -f tmp
 rm -f tmpj