For realizing how to utilize already quality checked masks

DiffusionPreprocessing/DiffPreprocPipeline.sh

@@ -544,6 +544,14 @@ main() {
 	log_Msg "eddy_cmd: ${eddy_cmd}"
 	${eddy_cmd}
 
+       echo """
+       Observe the following output files in ${StudyFolder}/${Subject}:
+       dwi:   Diffusion/eddy/eddy_unwarped_images.nii.gz
+       bvals: Diffusion/eddy/Pos_Neg.bvals
+       bvecs: Diffusion/eddy/eddy_unwarped_images.eddy_rotated_bvecs
+       mask:  Diffusion/eddy/nodif_brain_mask.nii.gz
+       """
+
     exit
 
 	log_Msg "Invoking Post-Eddy Steps"

DiffusionPreprocessing/scripts/eddy_pnl_repol.py

@@ -43,7 +43,7 @@ def main():
     if '--repol' in eddy_openmp_params and len(ind):
 
         print('\nDoing eddy_openmp/cuda again without --repol option '
-              'to obtain eddy correction w/o outlier replacement for b<=500 shells\n')
+              f'to obtain eddy correction w/o outlier replacement for b<={REPOL_BSHELL_GREATER} shells\n')
 
         eddy_openmp_params.remove('--repol')
         print(eddy_openmp_params)

DiffusionPreprocessing/scripts/run_eddy.sh

@@ -626,25 +626,24 @@ main() {
     # remove rawdata and release space
     rm -r ${workingdir}/../rawdata
 
-    # remove intensity normalized data
-    # rm ${workingdir}/Pos*
-    # rm ${workingdir}/Neg*
-
     # Redoing eddy without --repol flag to obtain not outlier replaced <=500 bshell
     if [ ! -z "${extra_eddy_args}" ]; then
-		for extra_eddy_arg in ${extra_eddy_args}; do
+	    for extra_eddy_arg in ${extra_eddy_args}; do
+
+		if [ $extra_eddy_arg = '--repol' ]; then
+                    log_Msg "Redoing eddy without --repol flag to obtain not outlier replaced b<=550 shells"
+                    eddy_command="${HCPPIPEDIR}/DiffusionPreprocessing/scripts/eddy_pnl_repol.py ${eddy_command}"
+                    log_Msg "${eddy_command}"
+                    ${eddy_command}
+                    eddyReturnValue=$?
+                    log_Msg "Completed with return value: ${eddyReturnValue}"
+		fi
 
-			if [ $extra_eddy_arg = '--repol' ]; then
-                log_Msg "Redoing eddy without --repol flag to obtain not outlier replaced b<=500 shells"
-                eddy_command="${HCPPIPEDIR}/DiffusionPreprocessing/scripts/eddy_pnl_repol.py ${eddy_command}"
-                log_Msg "${eddy_command}"
-                ${eddy_command}
-                eddyReturnValue=$?
-                log_Msg "Completed with return value: ${eddyReturnValue}"
-		    fi
+            done
+    fi
 
-        done
-	fi
+    # remove intensity normalized data
+    rm ${workingdir}/Pos_Neg.nii.gz
 
     exit ${eddyReturnValue}
 

DiffusionPreprocessing/scripts/run_topup.sh

@@ -14,16 +14,16 @@ ${FSLDIR}/bin/topup --imain=${workingdir}/Pos_Neg_b0 --datain=${workingdir}/acqp
 dimt=$(${FSLDIR}/bin/fslval ${workingdir}/Pos_b0 dim4)
 dimt=$((${dimt} + 1))
 
-# echo "Applying topup to get a hifi b0"
-# ${FSLDIR}/bin/fslroi ${workingdir}/Pos_b0 ${workingdir}/Pos_b01 0 1
-# ${FSLDIR}/bin/fslroi ${workingdir}/Neg_b0 ${workingdir}/Neg_b01 0 1
-# ${FSLDIR}/bin/applytopup --imain=${workingdir}/Pos_b01,${workingdir}/Neg_b01 --topup=${workingdir}/topup_Pos_Neg_b0 --datain=${workingdir}/acqparams.txt --inindex=1,${dimt} --out=${workingdir}/hifib0
-# 
-# if [ ! -f ${workingdir}/hifib0.nii.gz ]; then
-# 	echo "run_topup.sh -- ERROR -- ${FSLDIR}/bin/applytopup failed to generate ${workingdir}/hifib0.nii.gz"
-# 	# Need to add mechanism whereby scripts that invoke this script (run_topup.sh)
-# 	# check for a return code to determine success or failure
-# fi
+echo "Applying topup to get a hifi b0"
+${FSLDIR}/bin/fslroi ${workingdir}/Pos_b0 ${workingdir}/Pos_b01 0 1
+${FSLDIR}/bin/fslroi ${workingdir}/Neg_b0 ${workingdir}/Neg_b01 0 1
+${FSLDIR}/bin/applytopup --imain=${workingdir}/Pos_b01,${workingdir}/Neg_b01 --topup=${workingdir}/topup_Pos_Neg_b0 --datain=${workingdir}/acqparams.txt --inindex=1,${dimt} --out=${workingdir}/hifib0
+
+if [ ! -f ${workingdir}/hifib0.nii.gz ]; then
+	echo "run_topup.sh -- ERROR -- ${FSLDIR}/bin/applytopup failed to generate ${workingdir}/hifib0.nii.gz"
+	# Need to add mechanism whereby scripts that invoke this script (run_topup.sh)
+	# check for a return code to determine success or failure
+fi
 
 
 ${FSLDIR}/bin/imrm ${workingdir}/Pos_b0*
@@ -32,49 +32,29 @@ ${FSLDIR}/bin/imrm ${workingdir}/Neg_b0*
 # echo "Running BET on the hifi b0"
 # ${FSLDIR}/bin/bet ${workingdir}/hifib0 ${workingdir}/nodif_brain -m -f 0.2
 
-# echo "Applying PNL invented CNN masking tool to obtain b0 brain mask"
-# cnn_mask_exe=`which dwi_masking.py`
-# if [ ! -z $cnn_mask_exe ]; then
-#     echo "CNN-Diffusion-MRIBrain-Segmentation/pipeline/dwi_masking.py is not available in PATH"
-#     exit 1
-# fi
-# 
-# # TODO
-# $cnn_mask_exe -i ${workingdir}/hifib0 -f $(dirname $cnn_mask_exe)/../model_folder -o ${workingdir}/nodif_brain
-
-
-# define the masks in PA,AP order (pos,neg)
-# obtain 107 masks
-IFS=' ' read -ra masks_107 <<< $MASKS_107
-${FSLDIR}/bin/applytopup --imain=${masks_107[0]},${masks_107[1]} --topup=${workingdir}/topup_Pos_Neg_b0 --datain=${workingdir}/acqparams.txt --inindex=1,${dimt} --out=${workingdir}/mask_107 --verbose --method=jac --interp=trilinear
-
-# obtain 99 masks
-IFS=' ' read -ra masks_99 <<< $MASKS_99
-${FSLDIR}/bin/applytopup --imain=${masks_99[0]},${masks_99[1]} --topup=${workingdir}/topup_Pos_Neg_b0 --datain=${workingdir}/acqparams.txt --inindex=1,${dimt} --out=${workingdir}/mask_99 --verbose --method=jac --interp=trilinear
-
-# take their union
-pushd .
-cd ${workingdir}
-
-fslmaths mask_107 -abs mask_107
-fslmaths mask_99 -abs mask_99
-fslmaths mask_107 -add mask_99 nodif_brain_mask -odt char
-fslmaths nodif_brain_mask -bin nodif_brain_mask
-
-# filter the resultant mask
-if [ -z `which maskfilter.py` ]; then
-    echo "pnlNipype/scripts/maskfilter.py is not available in PATH"
+echo "Applying PNL invented CNN masking tool to obtain b0 brain mask"
+cnn_mask_exe=`which dwi_masking.py`
+if [ -z $cnn_mask_exe ]; then
+    echo "CNN-Diffusion-MRIBrain-Segmentation/pipeline/dwi_masking.py is not available in PATH"
     exit 1
 fi
-# maskfilter.py nodif_brain.nii.gz 2 nodif_brain.nii.gz
-
-${FSLDIR}/bin/imrm ${workingdir}/mask_107
-${FSLDIR}/bin/imrm ${workingdir}/mask_99
 
+pushd .
+cd ${workingdir}
+listpre=b0_list
+realpath hifib0.nii.gz > ${listpre}.txt
+$cnn_mask_exe -i ${listpre}.txt
+# rename
+mv hifib0_bse-multi_BrainMask.nii.gz nodif_brain_mask.nii.gz
+# cleanup
+rm ${listpre}*
+rm *_cases_*
+rm -r slicesdir_multi/
 popd
 
-if [ ! -f ${workingdir}/nodif_brain.nii.gz ]; then
-	echo "run_topup.sh -- ERROR -- ${FSLDIR}/bin/bet failed to generate ${workingdir}/nodif_brain.nii.gz"
+
+if [ ! -f ${workingdir}/nodif_brain_mask.nii.gz ]; then
+	echo "run_topup.sh -- ERROR -- CNN-Diffusion-MRIBrain-Segmentation/pipeline/dwi_masking.py failed to generate ${workingdir}/nodif_brain_mask.nii.gz"
 	# Need to add mechanism whereby scripts that invoke this script (run_topup.sh)
 	# check for a return code to determine success or failure
 fi