Switch to JSON project documentation, update versions

mrfil · Apr 1, 2022 · 1965cbd · 1965cbd
1 parent 7c4419f
commit 1965cbd
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/slurm_proc_7T_CUPS_step3.sh b/slurm_proc_7T_CUPS_step3.sh
@@ -83,14 +83,14 @@ sesname="ses-"${session}
 		SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} 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}
 
 		chmod 777 -R ${projDir}/bids/derivatives/qsiprep
-		${scripts}/pdf_printer.sh ${project} ${subject} ${sesname} QSIprep ${based}
+		SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --bind ${projDir}:/data,${scripts}:/scripts ${IMAGEDIR}/ubuntu-jqjo.sif /scripts//pdf_printer.sh ${project} ${subject} ${sesname} QSIprep ${based} "0.15.1"
 		NOW=$(date +"%m-%d-%Y-%T")
 		echo "QSIprep finished $NOW" >> ${scripts}/fulltimer.txt
 		NOW=$(date +"%m-%d-%Y-%T")
 		echo "QSIprep Recon started $NOW" >> ${scripts}/fulltimer.txt
-		SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} 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 ${subject}
-		SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} 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 ${subject}
-                SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} 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 ${subject}
+		SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} 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 mrtrix_multishell_msmt --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+		SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} 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 dsi_studio_gqi --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
+                SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} 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 amico_noddi --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
                 NOW=$(date +"%m-%d-%Y-%T")
 		echo "QSIprep Recon finished $NOW" >> ${scripts}/fulltimer.txt
 		chmod 777 -R ${projDir}/bids/derivatives/qsirecon