Washington-University · coalsont · Jan 11, 2021 · Dec 22, 2020 · Dec 22, 2020 · Dec 23, 2020
diff --git a/PostFreeSurfer/PostFreeSurferPipeline.sh b/PostFreeSurfer/PostFreeSurferPipeline.sh
@@ -80,19 +80,6 @@ fi
 #display the parsed/default values
 opts_ShowValues
 
-#processing code goes here
-
-verbose_red_echo "---> Starting ${log_ToolName}"
-verbose_echo " "
-verbose_echo " Using environment setting ..."
-verbose_echo "          HCPPIPEDIR: ${HCPPIPEDIR}"
-verbose_echo " "
-
-log_Check_Env_Var FSLDIR
-
-HCPPIPEDIR_PostFS="$HCPPIPEDIR/PostFreeSurfer/scripts"
-PipelineScripts="$HCPPIPEDIR_PostFS"
-
 doProcessing=1
 doQC=1
 
@@ -104,12 +91,26 @@ case "$QCMode" in
         ;;
     (only)
         doProcessing=0
+		log_Warn "Only generating structural QC scene and snapshots from existing data (no other processing)"
         ;;
     (*)
         log_Err_Abort "unrecognized value '$QCMode' for --structural-qc, use 'yes', 'no', or 'only'"
         ;;
 esac
 
+#processing code goes here
+
+verbose_red_echo "---> Starting ${log_ToolName}"
+verbose_echo " "
+verbose_echo " Using environment setting ..."
+verbose_echo "          HCPPIPEDIR: ${HCPPIPEDIR}"
+verbose_echo " "
+
+log_Check_Env_Var FSLDIR
+
+HCPPIPEDIR_PostFS="$HCPPIPEDIR/PostFreeSurfer/scripts"
+PipelineScripts="$HCPPIPEDIR_PostFS"
+
 # ------------------------------------------------------------------------------
 #  Naming Conventions
 #  Do NOT include spaces in any of these names
@@ -282,6 +283,7 @@ if ((doProcessing)); then
 fi
 
 if ((doQC)); then
+	log_Msg "Generating structural QC scene and snapshots"
     "$PipelineScripts"/GenerateStructuralScenes.sh \
         --study-folder="$StudyFolder" \
         --subject="$Subject" \

diff --git a/PostFreeSurfer/scripts/GenerateStructuralScenes.sh b/PostFreeSurfer/scripts/GenerateStructuralScenes.sh
@@ -301,3 +301,4 @@ done
 # Cleanup
 rm "$OutputSceneFolder/$Subject.$mapName."{L,R}".$mesh.func.gii"
 
+log_Msg "structural QC scene generation completed"
diff --git a/fMRISurface/GenericfMRISurfaceProcessingPipeline.sh b/fMRISurface/GenericfMRISurfaceProcessingPipeline.sh
@@ -35,6 +35,9 @@ Usage: ${script_name} [options]
   --smoothingFWHM=<smoothing FWHM (mm)>
   --grayordinatesres=<grayordinates res (mm)>
   [--regname=<surface registration name>] defaults to 'MSMSulc'
+  [--fmri-qc=<"YES|NO|ONLY">
+      Controls whether to generate a QC scene and snapshots (default=YES).
+      ONLY executes *just* the QC script, skipping everything else (e.g., for previous data)
 
 EOF
 }
@@ -94,13 +97,16 @@ FinalfMRIResolution=`opts_GetOpt1 "--fmrires" $@`
 SmoothingFWHM=`opts_GetOpt1 "--smoothingFWHM" $@`
 GrayordinatesResolution=`opts_GetOpt1 "--grayordinatesres" $@`
 RegName=`opts_GetOpt1 "--regname" $@`
-
-if [ -z "${RegName}" ]; then
-    RegName="MSMSulc"
-fi
+RegName=`opts_DefaultOpt $RegName MSMSulc`
+QCMode=`opts_GetOpt1 "--fmri-qc" $@`
+QCMode=`opts_DefaultOpt $QCMode YES`
+QCMode="$(echo ${QCMode} | tr '[:upper:]' '[:lower:]')"  # Convert to all lowercase
 
 RUN=`opts_GetOpt1 "--printcom" $@`  # use ="echo" for just printing everything and not running the commands (default is to run)
 
+doProcessing=1
+doQC=1
+
 log_Msg "Path: ${Path}"
 log_Msg "Subject: ${Subject}"
 log_Msg "NameOffMRI: ${NameOffMRI}"
@@ -109,6 +115,21 @@ log_Msg "FinalfMRIResolution: ${FinalfMRIResolution}"
 log_Msg "SmoothingFWHM: ${SmoothingFWHM}"
 log_Msg "GrayordinatesResolution: ${GrayordinatesResolution}"
 log_Msg "RegName: ${RegName}"
+log_Msg "QCMode: $QCMode"
+case "$QCMode" in
+    (yes)
+        ;;
+    (no)
+        doQC=0
+        ;;
+    (only)
+        doProcessing=0
+		log_Warn "Only generating fMRI QC scene and snapshots from existing data (no other processing)"
+        ;;
+    (*)
+        log_Err_Abort "unrecognized value '$QCMode' for --fmri-qc, use 'YES', 'NO', or 'ONLY'"
+        ;;
+esac
 log_Msg "RUN: ${RUN}"
 
 if [ "${RegName}" = "FS" ] ; then
@@ -139,25 +160,39 @@ T1wFolder="$Path"/"$Subject"/"$T1wFolder"
 ResultsFolder="$AtlasSpaceFolder"/"$ResultsFolder"/"$NameOffMRI"
 ROIFolder="$AtlasSpaceFolder"/"$ROIFolder"
 
-#Make fMRI Ribbon
-#Noisy Voxel Outlier Exclusion
-#Ribbon-based Volume to Surface mapping and resampling to standard surface
-
-log_Msg "Make fMRI Ribbon"
-log_Msg "mkdir -p ${ResultsFolder}/RibbonVolumeToSurfaceMapping"
-mkdir -p "$ResultsFolder"/RibbonVolumeToSurfaceMapping
-"$PipelineScripts"/RibbonVolumeToSurfaceMapping.sh "$ResultsFolder"/RibbonVolumeToSurfaceMapping "$ResultsFolder"/"$NameOffMRI" "$Subject" "$AtlasSpaceFolder"/"$DownSampleFolder" "$LowResMesh" "$AtlasSpaceFolder"/"$NativeFolder" "${RegName}"
-
-#Surface Smoothing
-log_Msg "Surface Smoothing"
-"$PipelineScripts"/SurfaceSmoothing.sh "$ResultsFolder"/"$NameOffMRI" "$Subject" "$AtlasSpaceFolder"/"$DownSampleFolder" "$LowResMesh" "$SmoothingFWHM"
+# ------------------------------------------------------------------------------
+#  Start work
+# ------------------------------------------------------------------------------
 
-#Subcortical Processing
-log_Msg "Subcortical Processing"
-"$PipelineScripts"/SubcorticalProcessing.sh "$AtlasSpaceFolder" "$ROIFolder" "$FinalfMRIResolution" "$ResultsFolder" "$NameOffMRI" "$SmoothingFWHM" "$GrayordinatesResolution"
+if ((doProcessing)); then
+    #Make fMRI Ribbon
+    #Noisy Voxel Outlier Exclusion
+    #Ribbon-based Volume to Surface mapping and resampling to standard surface
+	log_Msg "Make fMRI Ribbon"
+	log_Msg "mkdir -p ${ResultsFolder}/RibbonVolumeToSurfaceMapping"
+	mkdir -p "$ResultsFolder"/RibbonVolumeToSurfaceMapping
+	"$PipelineScripts"/RibbonVolumeToSurfaceMapping.sh "$ResultsFolder"/RibbonVolumeToSurfaceMapping "$ResultsFolder"/"$NameOffMRI" "$Subject" "$AtlasSpaceFolder"/"$DownSampleFolder" "$LowResMesh" "$AtlasSpaceFolder"/"$NativeFolder" "${RegName}"
+
+    #Surface Smoothing
+	log_Msg "Surface Smoothing"
+	"$PipelineScripts"/SurfaceSmoothing.sh "$ResultsFolder"/"$NameOffMRI" "$Subject" "$AtlasSpaceFolder"/"$DownSampleFolder" "$LowResMesh" "$SmoothingFWHM"
+
+    #Subcortical Processing
+	log_Msg "Subcortical Processing"
+	"$PipelineScripts"/SubcorticalProcessing.sh "$AtlasSpaceFolder" "$ROIFolder" "$FinalfMRIResolution" "$ResultsFolder" "$NameOffMRI" "$SmoothingFWHM" "$GrayordinatesResolution"
+
+    #Generation of Dense Timeseries
+	log_Msg "Generation of Dense Timeseries"
+	"$PipelineScripts"/CreateDenseTimeseries.sh "$AtlasSpaceFolder"/"$DownSampleFolder" "$Subject" "$LowResMesh" "$ResultsFolder"/"$NameOffMRI" "$SmoothingFWHM" "$ROIFolder" "$ResultsFolder"/"$OutputAtlasDenseTimeseries" "$GrayordinatesResolution"
+fi
 
-#Generation of Dense Timeseries
-log_Msg "Generation of Dense Timeseries"
-"$PipelineScripts"/CreateDenseTimeseries.sh "$AtlasSpaceFolder"/"$DownSampleFolder" "$Subject" "$LowResMesh" "$ResultsFolder"/"$NameOffMRI" "$SmoothingFWHM" "$ROIFolder" "$ResultsFolder"/"$OutputAtlasDenseTimeseries" "$GrayordinatesResolution"
+if ((doQC)); then
+    log_Msg "Generating fMRI QC scene and snapshots"
+    "$PipelineScripts"/GenerateFMRIScenes.sh \
+        --study-folder="$Path" \
+        --subject="$Subject" \
+        --fmriname="$NameOffMRI" \
+        --output-folder="$ResultsFolder/fMRIQC"
+fi
 
 log_Msg "Completed!"
diff --git a/fMRIVolume/scripts/GenerateFMRIScenes.sh → fMRISurface/scripts/GenerateFMRIScenes.sh b/fMRIVolume/scripts/GenerateFMRIScenes.sh → fMRISurface/scripts/GenerateFMRIScenes.sh
@@ -73,9 +73,9 @@ OutputSceneFolder=$(cd "$OutputSceneFolder"; pwd)
 # ----------------------------
 
 # The following are matched to actual strings in the TEMPLATE_fMRIQC.scene file
-StudyFolderDummyStr="StudyFolder"
-SubjectIDDummyStr="SubjectID"
-fMRINameDummyStr="fMRIName"
+StudyFolderDummyStr="STUDYDIR"
+SubjectIDDummyStr="SESSION"
+fMRINameDummyStr="FMRINAME"
 
 # ----------------------------
 # Begin main action of script
@@ -94,20 +94,20 @@ fi
 
 # Replace dummy strings in the template scenes to generate
 # a scene file appropriate for each subject and fMRI run
-sceneFile="$OutputSceneFolder/${Subject}_${fMRIName}.fMRIQC.wb_scene"
+sceneFile="${Subject}_${fMRIName}.fMRIQC.wb_scene"  # No path (file name only)
 sed -e "s|${StudyFolderDummyStr}|${relPathToStudy}|g" \
     -e "s|${SubjectIDDummyStr}|${Subject}|g" \
     -e "s|${fMRINameDummyStr}|${fMRIName}|g" \
-    "$TemplatesFolder"/TEMPLATE_fMRIQC.scene > "$sceneFile"
+    "$TemplatesFolder"/TEMPLATE_fMRIQC.scene > "$OutputSceneFolder/$sceneFile"
 
 # Generate snapshots
 pngDir="$OutputSceneFolder/snapshots"
 mkdir -p "${pngDir}"
 #numScenes=$(grep "SceneInfo Index" "$OutputSceneFolder/$sceneFile" | wc -l)
 #for ((ind = 1; ind <= numScenes; ind++)); do
 scenesToCapture="1 2"
-for $ind in $scenesToCapture; do
+for ind in $scenesToCapture; do
     wb_command -show-scene "$OutputSceneFolder/$sceneFile" $ind "${pngDir}/${sceneFile}${ind}.png" 1400 600 -logging OFF
 done
 
-log_Msg "fMRI scene generation completed"
+log_Msg "fMRI QC scene generation completed"
diff --git a/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh b/fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh
@@ -130,11 +130,6 @@ Usage: ${script_name} [options]
       is NOT applied, regardless of value).  
       Default: "TRUE" if using --dcmethod="${SPIN_ECHO_METHOD_OPT}"; "FALSE" for all other SDC methods.
 
-  [--fmri-qc=<"YES|NO|ONLY">
-
-      Controls whether to generate a QC scene and snapshots (YES=default).
-      ONLY executes *just* the QC script, skipping everything else (e.g., for previous data)
-
   [--processing-mode=<"HCPStyleData" (default) or "LegacyStyleData">
 
       Controls whether the HCP acquisition and processing guidelines should be treated as requirements.
@@ -573,18 +568,6 @@ then
 	log_Err_Abort "the --usejacobian option must be 'true' or 'false'"
 fi
 
-QCMode=`opts_GetOpt1 "--fmri-qc" $@`
-QCMode=`opts_DefaultOpt $QCMode YES`
-QCMode="$(echo ${QCMode} | tr '[:upper:]' '[:lower:]')"  # Convert to all lowercase
-case "$QCMode" in
-    (yes|no|only)
-        log_Msg "QCMode: $QCMode"
-        ;;
-    (*)
-        log_Err_Abort "unrecognized value '$QCMode' for --fmri-qc, use 'YES', 'NO', or 'ONLY'"
-        ;;
-esac
-
 RUN=`opts_GetOpt1 "--printcom" $@`  # use ="echo" for just printing everything and not running the commands (default is to run)
 log_Msg "RUN: ${RUN}"
 
@@ -831,16 +814,6 @@ T1wFolder="$Path"/"$Subject"/"$T1wFolder"
 AtlasSpaceFolder="$Path"/"$Subject"/"$AtlasSpaceFolder"
 ResultsFolder="$AtlasSpaceFolder"/"$ResultsFolder"/"$NameOffMRI"
 
-if [[ $QCMode == "only" ]] ; then  # Generate QC scene and return
-    log_Msg "Generating fMRI QC scene and snapshots, then exiting"
-    "$PipelineScripts"/GenerateFMRIScenes.sh \
-        --study-folder="$Path" \
-        --subject="$Subject" \
-        --fmriname="$NameOffMRI"
-        --output-folder="$ResultsFolder/fMRIQC"
-    return
-fi
-
 mkdir -p ${T1wFolder}/Results/${NameOffMRI}
 
 if [ ! -e "$fMRIFolder" ] ; then
@@ -1149,16 +1122,6 @@ ${RUN} cp ${fMRIFolder}/Movement_AbsoluteRMS.txt ${ResultsFolder}
 ${RUN} cp ${fMRIFolder}/Movement_RelativeRMS_mean.txt ${ResultsFolder}
 ${RUN} cp ${fMRIFolder}/Movement_AbsoluteRMS_mean.txt ${ResultsFolder}
 
-# Generate fMRIQC scene and snapshots
-if [[ $QCMode == "yes" ]] ; then
-    log_Msg "Generating fMRI QC scene and snapshots"
-    "$PipelineScripts"/GenerateFMRIScenes.sh \
-        --study-folder="$Path" \
-        --subject="$Subject" \
-        --fmriname="$NameOffMRI"
-        --output-folder="$ResultsFolder/fMRIQC"
-fi
-
 #Basic Cleanup
 ${FSLDIR}/bin/imrm ${fMRIFolder}/${NameOffMRI}_nonlin_norm
 

diff --git a/global/templates/fMRIQC/TEMPLATE_fMRIQC.scene b/global/templates/fMRIQC/TEMPLATE_fMRIQC.scene
Original file line number	Diff line number	Diff line change
Expand Up		@@ -301,3 +301,4 @@ done
		# Cleanup
		rm "$OutputSceneFolder/$Subject.$mapName."{L,R}".$mesh.func.gii"

		log_Msg "structural QC scene generation completed"