HCP HippUnfold and Post HippUnfold Implementations

Examples/Scripts/RunHippUnfoldHCP.sh

@@ -0,0 +1,94 @@
+#!/bin/bash 
+
+get_batch_options() {
+    local arguments=("$@")
+
+    command_line_specified_study_folder=""
+    command_line_specified_subject=""
+    command_line_specified_run_local="FALSE"
+
+    local index=0
+    local numArgs=${#arguments[@]}
+    local argument
+
+    while [ ${index} -lt ${numArgs} ]; do
+        argument=${arguments[index]}
+
+        case ${argument} in
+            --StudyFolder=*)
+                command_line_specified_study_folder=${argument#*=}
+                index=$(( index + 1 ))
+                ;;
+            --Subject=*)
+                command_line_specified_subject=${argument#*=}
+                index=$(( index + 1 ))
+                ;;
+            --runlocal)
+                command_line_specified_run_local="TRUE"
+                index=$(( index + 1 ))
+                ;;
+	    *)
+		echo ""
+		echo "ERROR: Unrecognized Option: ${argument}"
+		echo ""
+		exit 1
+		;;
+        esac
+    done
+}
+
+get_batch_options "$@"
+
+StudyFolder="${HOME}/projects/Pipelines_ExampleData" #Location of Subject folders (named by SubjectID) 
+Subjlist="100307 100610" #Space delimited list of subject IDs 
+EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script 
+
+if [ -n "${command_line_specified_study_folder}" ]; then
+    StudyFolder="${command_line_specified_study_folder}"
+fi
+
+if [ -n "${command_line_specified_subject}" ]; then
+    Subjlist="${command_line_specified_subject}"
+fi
+
+#Set up pipeline environment variables and software
+source "$EnvironmentScript"
+
+# Log the originating call
+echo "$@"
+
+#NOTE: syntax for QUEUE has changed compared to earlier pipeline releases,
+#DO NOT include "-q " at the beginning
+#default to no queue, implying run local
+QUEUE=""
+#QUEUE="hcp_priority.q"
+
+########################################## INPUTS ########################################## 
+
+#Scripts called by this script do assume they run on the outputs of the PostFreeSurfer Pipeline
+
+######################################### DO WORK ##########################################
+
+for Subject in $Subjlist ; do
+  echo $Subject
+
+  if [[ "${command_line_specified_run_local}" == "TRUE" || "$QUEUE" == "" ]] ; then
+      echo "About to locally run ${HCPPIPEDIR}/HippUnfoldHCP/HippUnfoldHCP.sh"
+      queuing_command=("$HCPPIPEDIR"/global/scripts/captureoutput.sh)
+  else
+      echo "About to use fsl_sub to queue ${HCPPIPEDIR}/HippUnfoldHCP/HippUnfoldHCP.sh"
+      queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE")
+  fi
+
+  "${queuing_command[@]}" "$HCPPIPEDIR"/HippUnfoldHCP/HippUnfoldHCP.sh \
+      --study-folder="$StudyFolder" \
+      --subject="$Subject" \
+
+  # The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 ...
+
+  echo "set -- --study-folder=$StudyFolder \
+      --subject=$Subject" \
+
+  echo ". ${EnvironmentScript}"
+
+done

Examples/Scripts/RunPostHippUnfoldHCP.sh

@@ -0,0 +1,94 @@
+#!/bin/bash 
+
+get_batch_options() {
+    local arguments=("$@")
+
+    command_line_specified_study_folder=""
+    command_line_specified_subject=""
+    command_line_specified_run_local="FALSE"
+
+    local index=0
+    local numArgs=${#arguments[@]}
+    local argument
+
+    while [ ${index} -lt ${numArgs} ]; do
+        argument=${arguments[index]}
+
+        case ${argument} in
+            --StudyFolder=*)
+                command_line_specified_study_folder=${argument#*=}
+                index=$(( index + 1 ))
+                ;;
+            --Subject=*)
+                command_line_specified_subject=${argument#*=}
+                index=$(( index + 1 ))
+                ;;
+            --runlocal)
+                command_line_specified_run_local="TRUE"
+                index=$(( index + 1 ))
+                ;;
+	    *)
+		echo ""
+		echo "ERROR: Unrecognized Option: ${argument}"
+		echo ""
+		exit 1
+		;;
+        esac
+    done
+}
+
+get_batch_options "$@"
+
+StudyFolder="${HOME}/projects/Pipelines_ExampleData" #Location of Subject folders (named by SubjectID) 
+Subjlist="100307 100610" #Space delimited list of subject IDs 
+EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script 
+
+if [ -n "${command_line_specified_study_folder}" ]; then
+    StudyFolder="${command_line_specified_study_folder}"
+fi
+
+if [ -n "${command_line_specified_subject}" ]; then
+    Subjlist="${command_line_specified_subject}"
+fi
+
+#Set up pipeline environment variables and software
+source "$EnvironmentScript"
+
+# Log the originating call
+echo "$@"
+
+#NOTE: syntax for QUEUE has changed compared to earlier pipeline releases,
+#DO NOT include "-q " at the beginning
+#default to no queue, implying run local
+QUEUE=""
+#QUEUE="hcp_priority.q"
+
+########################################## INPUTS ########################################## 
+
+#Scripts called by this script do assume they run on the outputs of the PostFreeSurfer Pipeline
+
+######################################### DO WORK ##########################################
+
+for Subject in $Subjlist ; do
+  echo $Subject
+
+  if [[ "${command_line_specified_run_local}" == "TRUE" || "$QUEUE" == "" ]] ; then
+      echo "About to locally run ${HCPPIPEDIR}/HippUnfoldHCP/PostHippUnfoldHCP.sh"
+      queuing_command=("$HCPPIPEDIR"/global/scripts/captureoutput.sh)
+  else
+      echo "About to use fsl_sub to queue ${HCPPIPEDIR}/HippUnfoldHCP/PostHippUnfoldHCP.sh"
+      queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE")
+  fi
+
+  "${queuing_command[@]}" "$HCPPIPEDIR"/HippUnfoldHCP/PostHippUnfoldHCP.sh \
+      --study-folder="$StudyFolder" \
+      --subject="$Subject" \
+
+  # The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 ...
+
+  echo "set -- --study-folder=$StudyFolder \
+      --subject=$Subject" \
+
+  echo ". ${EnvironmentScript}"
+
+done

Examples/Scripts/SetUpHCPPipeline.sh

@@ -26,6 +26,8 @@ export MATLAB_COMPILER_RUNTIME=/export/matlab/MCR/R2017b/v93
 # If a suitable version of wb_command is on your $PATH, CARET7DIR can be blank
 export CARET7DIR=
 export HCPCIFTIRWDIR="$HCPPIPEDIR"/global/matlab/cifti-matlab
+export HIPPUNFOLDPATH="${HOME}/pipeline_tools/HippUnfold/khanlab_hippunfold_latest.sif"
+export HIPPUNFOLD_CACHE_DIR="${HOME}/.cache/hippunfold"
 
 ## Set up FSL (if not already done so in the running environment)
 ## Uncomment the following 2 lines (remove the leading #) and correct the FSLDIR setting for your setup

HippUnfoldHCP/HippUnfoldHCP.sh

@@ -0,0 +1,101 @@
+#!/bin/bash
+set -eu
+pipedirguessed=0
+if [[ "${HCPPIPEDIR:-}" == "" ]]
+then
+  # pipedirguessed=1
+   #fix this if the script is more than one level below HCPPIPEDIR
+   export HCPPIPEDIR="$(dirname -- "$0")/.."
+fi
+
+source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
+source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
+
+
+opts_SetScriptDescription "Make some BIDS structures and run HippUnfold"
+
+opts_AddMandatory '--study-folder' 'StudyFolder' 'path' "folder containing all subjects"
+opts_AddMandatory '--subject' 'Subject' 'subject ID' ""
+opts_AddOptional '--hippunfold-dir' 'HippUnfoldDIR' 'path' "location of HippUnfold outputs"
+
+opts_ParseArguments "$@"
+
+if ((pipedirguessed))
+then
+    log_Err_Abort "HCPPIPEDIR is not set, you must first source your edited copy of Examples/Scripts/SetUpHCPPipeline.sh"
+fi
+
+opts_ShowValues
+
+T1wFolder="$StudyFolder/$Subject/T1w"       # input data
+
+if [ -z ${HippUnfoldDIR} ] ; then
+  HippUnfoldDIR="${T1wFolder}/HippUnfold"
+fi 
+
+#Couldn't get non-BIDS to work (wouldn't do anything)
+#HippUnfoldT1wFolder="$HippUnfoldDIR/T1w"
+#HippUnfoldT2wFolder="$HippUnfoldDIR/T2w"
+#HippUnfoldT2wFolder="$HippUnfoldDIR/T1wT2w"
+
+HippUnfoldT1wFolder="$HippUnfoldDIR/T1w/sub-${Subject}/anat"
+HippUnfoldT2wFolder="$HippUnfoldDIR/T2w/sub-${Subject}/anat"
+HippUnfoldT1wT2wFolder="$HippUnfoldDIR/T1wT2w/sub-${Subject}/anat"
+
+HippUnfoldT1wFolderOut="$HippUnfoldDIR/T1w_hippunfold"
+HippUnfoldT2wFolderOut="$HippUnfoldDIR/T2w_hippunfold"
+HippUnfoldT1wT2wFolderOut="$HippUnfoldDIR/T1wT2w_hippunfold"
+
+
+T1wImage="$T1wFolder/T1w_acpc_dc_restore.nii.gz"
+T2wImage="$T1wFolder/T2w_acpc_dc_restore.nii.gz"
+
+
+if [ ! -f "$T1wImage" ]; then
+    echo "Error: T1w image not found at $T1wImage" >&2
+    exit 1
+fi
+
+if [ ! -f "$T2wImage" ]; then
+    echo "Error: T2w image not found at $T2wImage" >&2
+    exit 1
+fi
+
+
+mkdir -p "$HippUnfoldT1wFolder" "$HippUnfoldT2wFolder" "$HippUnfoldT1wT2wFolder"
+
+#Couldn't get non-BIDS to work (wouldn't do anything)
+#cp "$T1wImage" "$HippUnfoldT1wFolder/${Subject}_T1w_acpc_dc_restore.nii.gz"
+#cp "$T2wImage" "$HippUnfoldT1wFolder/${Subject}_T2w_acpc_dc_restore.nii.gz"
+#cp "$T1wImage" "$HippUnfoldT2wFolder/${Subject}_T1w_acpc_dc_restore.nii.gz"
+#cp "$T2wImage" "$HippUnfoldT2wFolder/${Subject}_T2w_acpc_dc_restore.nii.gz"
+#cp "$T1wImage" "$HippUnfoldT1wT2wFolder/${Subject}_T1w_acpc_dc_restore.nii.gz"
+#cp "$T2wImage" "$HippUnfoldT1wT2wFolder/${Subject}_T2w_acpc_dc_restore.nii.gz"
+
+cp "$T1wImage" "$HippUnfoldT1wFolder/sub-${Subject}_T1w.nii.gz"
+cp "$T2wImage" "$HippUnfoldT1wFolder/sub-${Subject}_T2w.nii.gz"
+cp "$T1wImage" "$HippUnfoldT2wFolder/sub-${Subject}_T1w.nii.gz"
+cp "$T2wImage" "$HippUnfoldT2wFolder/sub-${Subject}_T2w.nii.gz"
+cp "$T1wImage" "$HippUnfoldT1wT2wFolder/sub-${Subject}_T1w.nii.gz"
+cp "$T2wImage" "$HippUnfoldT1wT2wFolder/sub-${Subject}_T2w.nii.gz"
+
+
+log_Msg "Created folder structure under $HippUnfoldDIR and copied T1w and T2w images"
+log_Msg "Starting HippUnfold pipeline for subject: $Subject"
+
+#Couldn't get non-BIDS to work (wouldn't do anything)                                                                                                     #Seriously: don't put a $ here...
+#apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT1wFolder $HippUnfoldT1wFolder participant --modality T1w --path-T1w $HippUnfoldT1wFolder/{Subject}_T1w_acpc_dc_restore.nii.gz --cores all --force-output --generate_myelin_map
+#apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT2wFolder $HippUnfoldT2wFolder participant --modality T2w --path-T2w $HippUnfoldT2wFolder/{Subject}_T2w_acpc_dc_restore.nii.gz --cores all --force-output --generate_myelin_map
+#apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT2wFolder $HippUnfoldT2wFolder participant --modality T2w --path-T2w $HippUnfoldT2wFolder/{Subject}_T2w_acpc_dc_restore.nii.gz --cores all --force-output --generate_myelin_map --force-nnunet-model T1T2w
+
+log_Msg "Running T1w HippUnfold for subject: $Subject"
+apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT1wFolder $HippUnfoldT1wFolderOut participant --modality T1w --cores all --force-output --generate_myelin_map --output-density 0p5mm 1mm 2mm
+log_Msg "T1w HippUnfold completed."
+log_Msg "Running T2w HippUnfold for subject: $Subject"
+apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT2wFolder $HippUnfoldT2wFolderOut participant --modality T2w --cores all --force-output --generate_myelin_map --output-density 0p5mm 1mm 2mm
+log_Msg "T2w HippUnfold completed."
+log_Msg "Running T1wT2w HippUnfold for subject: $Subject"
+apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT1wT2wFolder $HippUnfoldT1wT2wFolderOut participant --modality T1w --cores all --force-output --generate_myelin_map --output-density 0p5mm 1mm 2mm --force-nnunet-model T1T2w
+log_Msg "T1wT2w HippUnfold completed."
+
+log_Msg "HippUnfold pipeline completed successfully for subject: $Subject"