Structural longitudinal pipelines

Examples/Scripts/FreeSurferPipelineBatch-long.sh

@@ -0,0 +1,139 @@
+#!/bin/bash
+
+command_line_specified_run_local=FALSE
+while [ -n "$1" ]; do
+    case "$1" in
+        --runlocal) shift; command_line_specified_run_local=TRUE ;;
+        *) shift ;;
+    esac
+done
+
+#################################################################################################
+# General input variables
+##################################################################################################
+#Location of Subject folders (named by subjectID)
+StudyFolder="/my/study/path"
+#The list of subject labels, space separated
+Subjects=(HCA6002236 HCA6002237 HCA6002238)
+#The list of possible visits (aka timepoints, sessions) that each subject may have. Timepoint directories should be named <Subject>_<Visit>.
+PossibleVisits=(V1_MR V2_MR V3_MR)
+#The list of possible visits that each subject may have. Timepoint (visit) is expected to be named <Subject>_<Visit>.
+#Actual visits (timepoints) are determined based on existing directories that match the visit name pattern.
+#ExcludeVisits=(HCA6002237_V1_MR HCA6002238_V1_MR)
+ExcludeVisits=()
+#Longitudinal template labels, one per each subject.
+Templates=(HCA6002236_V1_V2 HCA6002237_V1_V2 HCA6002238_V1_V2)
+
+EnvironmentScript="<HCPInstallDir>/scripts/SetUpHCPPipeline.sh" #Pipeline environment script
+
+# Requirements for this script
+#  installed versions of: FSL, FreeSurfer, Connectome Workbench (wb_command), gradunwarp (HCP version)
+#  environment: HCPPIPEDIR, FSLDIR, FREESURFER_HOME, CARET7DIR, PATH for gradient_unwarp.py
+
+# If you want to use FreeSurfer 5.3, change the ${queuing_command} line below to use
+# ${HCPPIPEDIR}/FreeSurfer/FreeSurferPipeline-v5.3.0-HCP.sh
+
+#Set up pipeline environment variables and software
+source "$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="long.q"
+#QUEUE="hcp_priority.q"
+
+#parallel options
+parallel_mode=BUILTIN
+
+# This setting is for BUILTIN mode. Set to -1 to auto-detect the # of CPU cores on the node where each per-subject job is run.
+# Note that in case when multiple subject jobs are run on the same node and are submitted 
+# in parallel by e.g. fsl_sub, max_jobs should be set manually to not significantly exceed
+# (number of available cores)/(number of subjects) in the batch. 
+max_jobs=-1
+#max_jobs=4
+
+#TEMPLATE stage must be run before TIMEPOINTS stage
+start_stage=TEMPLATE
+end_stage=TIMEPOINTS
+
+#Processing goes here.
+function identify_timepoints
+{
+    local subject=$1
+    local tplist=""
+    local tp visit n
+
+    #build the list of timepoints (sessions)
+    n=0
+    for session in ${PossibleVisits[*]}; do
+        tp="${subject}_${session}"
+        if [ -d "$StudyFolder/$tp" ] && ! [[ " ${ExcludeVisits[*]+${ExcludeVisits[*]}} " =~ [[:space:]]"$tp"[[:space:]] ]]; then
+             if (( n==0 )); then 
+                    tplist="$tp"
+             else
+                    tplist="$tplist@$tp"
+             fi
+        fi
+        ((n++))
+    done
+    echo $tplist
+}
+
+########################################## INPUTS ########################################## 
+#Scripts called by this script do assume they run on the outputs of the PreFreeSurfer Pipeline
+######################################### DO WORK ##########################################
+
+for i in ${!Subjects[@]}; do
+  Subject=${Subjects[i]}
+  #Subject's time point list, @ separated.  
+  TPlist=(`identify_timepoints $Subject`)
+  #Array with timepoints
+  IFS=@ read -ra Timepoints <<< "$TPlist"
+  #Freesurfer longitudinal average template label
+  LongitudinalTemplate=${Templates[i]}
+
+  #Longitudinal FreeSurfer Input Variables
+  SubjectID="$Subject" #FreeSurfer Subject ID Name
+  SubjectDIR="${StudyFolder}/${Subject}/T1w" #Location to Put FreeSurfer Subject's Folder
+  T1wImage="${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore.nii.gz" #T1w FreeSurfer Input (Full Resolution)
+  T1wImageBrain="${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore_brain.nii.gz" #T1w FreeSurfer Input (Full Resolution)
+  T2wImage="${StudyFolder}/${Subject}/T1w/T2w_acpc_dc_restore.nii.gz" #T2w FreeSurfer Input (Full Resolution)
+
+  if [ "$parallel_mode" != FSLSUB ]; then #fsl_sub does not allow nested submissions
+    if [[ "${command_line_specified_run_local}" == "TRUE" || "$QUEUE" == "" ]] ; then
+        echo "About to locally run ${HCPPIPEDIR}/FreeSurfer/LongitudinalFreeSurferPipeline.sh"
+        #NOTE: fsl_sub without -q runs locally and captures output in files
+        queuing_command=("$FSLDIR/bin/fsl_sub")
+    else
+        echo "About to use fsl_sub to queue ${HCPPIPEDIR}/FreeSurfer/LongitudinalFreeSurferPipeline.sh"
+        queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE")
+    fi
+  else
+    queuing_command=()
+  fi
+
+  #DO NOT PUT timepoint-specific options here!!!
+  cmd=(${queuing_command[@]+"${queuing_command[@]}"} "$HCPPIPEDIR"/FreeSurfer/LongitudinalFreeSurferPipeline.sh \
+    --subject="$Subject" \
+    --path="$StudyFolder" \
+    --sessions="$TPlist" \
+    --fslsub-queue="$QUEUE" \
+    --longitudinal-template="$LongitudinalTemplate" \
+    --parallel-mode="$parallel_mode" \
+    --max-jobs="$max_jobs" \
+    --start-stage="$start_stage" \
+    --end-stage="$end_stage" \
+    )
+
+  #--extra-reconall-arg-base=-conf2hires Freesurfer reports this is unneeded.
+  echo "Running command: ${cmd[*]}"
+  "${cmd[@]}"
+
+  # The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 ...
+  # echo set --subject=$Subject --subjectDIR=$SubjectDIR --t1=$T1wImage --t1brain=$T1wImageBrain --t2=$T2wImage --extra-reconall-arg-long="-i \"$SubjectDIR\"/T1w/T1w_acpc_dc_restore.nii.gz -emregmask \"$SubjectDIR\"/T1w/T1w_acpc_dc_restore_brain.nii.gz -T2 $SubjectDIR\"/T1w/T2w_acpc_dc_restore.nii.gz -T2pial"
+  #echo ". ${EnvironmentScript}"
+
+done

Examples/Scripts/FreeSurferPipelineBatch.sh

@@ -4,7 +4,7 @@ get_batch_options() {
     local arguments=("$@")
 
     command_line_specified_study_folder=""
-    command_line_specified_subj=""
+    command_line_specified_session=""
     command_line_specified_run_local="FALSE"
 
     local index=0
@@ -19,8 +19,12 @@ get_batch_options() {
                 command_line_specified_study_folder=${argument#*=}
                 index=$(( index + 1 ))
                 ;;
-            --Subject=*)
-                command_line_specified_subj=${argument#*=}
+            --Subject=*) #legacy option, please use '--Session' instead
+                command_line_specified_session=${argument#*=}
+                index=$(( index + 1 ))
+                ;;
+            --Session=*)
+                command_line_specified_session=${argument#*=}
                 index=$(( index + 1 ))
                 ;;
             --runlocal)
@@ -39,16 +43,16 @@ get_batch_options() {
 
 get_batch_options "$@"
 
-StudyFolder="${HOME}/projects/Pipelines_ExampleData" #Location of Subject folders (named by subjectID) 
-Subjlist="100307 100610" #Space delimited list of subject IDs 
+StudyFolder="${HOME}/projects/Pipelines_ExampleData" #Location of Session folders (named by sessionID) 
+Sessionlist="100307 100610" #Space delimited list of session 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 "${command_line_specified_subj}" ]; then
-    Subjlist="${command_line_specified_subj}"
+if [ -n "${command_line_specified_session}" ]; then
+    Sessionlist="${command_line_specified_session}"
 fi
 
 # Requirements for this script
@@ -76,15 +80,15 @@ QUEUE=""
 
 ######################################### DO WORK ##########################################
 
-for Subject in $Subjlist ; do
-  echo $Subject
+for Session in $Sessionlist ; do
+  echo $Session
 
   #Input Variables
-  SubjectID="$Subject" #FreeSurfer Subject ID Name
-  SubjectDIR="${StudyFolder}/${Subject}/T1w" #Location to Put FreeSurfer Subject's Folder
-  T1wImage="${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore.nii.gz" #T1w FreeSurfer Input (Full Resolution)
-  T1wImageBrain="${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore_brain.nii.gz" #T1w FreeSurfer Input (Full Resolution)
-  T2wImage="${StudyFolder}/${Subject}/T1w/T2w_acpc_dc_restore.nii.gz" #T2w FreeSurfer Input (Full Resolution)
+  SessionID="$Session" #FreeSurfer Subject ID Name
+  SessionDIR="${StudyFolder}/${Session}/T1w" #Location to Put FreeSurfer Subject's Folder
+  T1wImage="${StudyFolder}/${Session}/T1w/T1w_acpc_dc_restore.nii.gz" #T1w FreeSurfer Input (Full Resolution)
+  T1wImageBrain="${StudyFolder}/${Session}/T1w/T1w_acpc_dc_restore_brain.nii.gz" #T1w FreeSurfer Input (Full Resolution)
+  T2wImage="${StudyFolder}/${Session}/T1w/T2w_acpc_dc_restore.nii.gz" #T2w FreeSurfer Input (Full Resolution)
 
   if [[ "${command_line_specified_run_local}" == "TRUE" || "$QUEUE" == "" ]] ; then
       echo "About to locally run ${HCPPIPEDIR}/FreeSurfer/FreeSurferPipeline.sh"
@@ -95,16 +99,16 @@ for Subject in $Subjlist ; do
   fi
 
   "${queuing_command[@]}" "$HCPPIPEDIR"/FreeSurfer/FreeSurferPipeline.sh \
-      --subject="$Subject" \
-      --subject-dir="$SubjectDIR" \
+      --session="$Session" \
+      --session-dir="$SessionDIR" \
       --t1w-image="$T1wImage" \
       --t1w-brain="$T1wImageBrain" \
       --t2w-image="$T2wImage"
 
   # The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 ...
 
-  echo "set -- --subject=$Subject \
-      --subject-dir=$SubjectDIR \
+  echo "set -- --session=$Session \
+      --session-dir=$SessionDIR \
       --t1w-image=$T1wImage \
       --t1w-brain=$T1wImageBrain \
       --t2w-image=$T2wImage"

Examples/Scripts/PostFreeSurferPipelineBatch-long.sh

@@ -0,0 +1,169 @@
+#!/bin/bash 
+
+command_line_specified_run_local=FALSE
+while [ -n "$1" ]; do
+    case "$1" in
+        --runlocal) shift; command_line_specified_run_local=TRUE ;;
+        *) shift ;;
+    esac
+done
+
+#################################################################################################
+# General input variables
+##################################################################################################
+#Location of Subject folders (named by subjectID)
+StudyFolder="<MyStudyPath>"
+#The list of subject labels, space separated
+Subjects=(HCA6002236 HCA6002237 HCA6002238)
+#The list of possible visits that each subject may have. Timepoint (visit) is expected to be named <Subject>_<Visit>.
+PossibleVisits=(V1_MR V2_MR V3_MR)
+#Actual visits (timepoints) are determined based on existing directories that match the visit name pattern <Subject>_<visit>.
+#Excluded timepoint directories
+#ExcludeVisits=(HCA6002237_V1_MR HCA6002238_V1_MR)
+ExcludeVisits=()
+#Longitudinal template labels, one per each subject.
+Templates=(HCA6002236_V1_V2 HCA6002237_V1_V2 HCA6002238_V1_V2)
+#EnvironmentScript="${HOME}/projects/HCPPipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script
+EnvironmentScript="${HOME}/projects/HCPPipelines/Examples/Scripts/SetUpHCPPipeline.sh"
+source "$EnvironmentScript"
+
+##################################################################################################
+# Input variables used by PostFreeSurferPipelineLongPrep
+##################################################################################################
+# Hires T1w MNI template
+T1wTemplate="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm.nii.gz"
+# Hires brain extracted MNI template1
+T1wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm_brain.nii.gz"
+# Lowres T1w MNI template
+T1wTemplate2mm="${HCPPIPEDIR_Templates}/MNI152_T1_2mm.nii.gz"
+# Hires T2w MNI Template
+T2wTemplate="${HCPPIPEDIR_Templates}/MNI152_T2_0.8mm.nii.gz"
+# Hires T2w brain extracted MNI Template
+T2wTemplateBrain="${HCPPIPEDIR_Templates}/MNI152_T2_0.8mm_brain.nii.gz"
+# Lowres T2w MNI Template
+T2wTemplate2mm="${HCPPIPEDIR_Templates}/MNI152_T2_2mm.nii.gz"
+# Hires MNI brain mask template
+TemplateMask="${HCPPIPEDIR_Templates}/MNI152_T1_0.8mm_brain_mask.nii.gz"
+# Lowres MNI brain mask template
+Template2mmMask="${HCPPIPEDIR_Templates}/MNI152_T1_2mm_brain_mask_dil.nii.gz"
+# FNIRT 2mm T1w Config
+FNIRTConfig="${HCPPIPEDIR_Config}/T1_2_MNI152_2mm.cnf"
+
+##################################################################################################
+# Input variables used by PostFreesurferPipeline (longitudinal mode)
+##################################################################################################
+SurfaceAtlasDIR="${HCPPIPEDIR_Templates}/standard_mesh_atlases"
+GrayordinatesSpaceDIR="${HCPPIPEDIR_Templates}/91282_Greyordinates"
+GrayordinatesResolutions="2" #Usually 2mm, if multiple delimit with @, must already exist in templates dir
+HighResMesh="164" #Usually 164k vertices
+LowResMeshes="32" #Usually 32k vertices, if multiple delimit with @, must already exist in templates dir
+SubcorticalGrayLabels="${HCPPIPEDIR_Config}/FreeSurferSubcorticalLabelTableLut.txt"
+FreeSurferLabels="${HCPPIPEDIR_Config}/FreeSurferAllLut.txt"
+ReferenceMyelinMaps="${HCPPIPEDIR_Templates}/standard_mesh_atlases/Conte69.MyelinMap_BC.164k_fs_LR.dscalar.nii"
+RegName="MSMSulc" #MSMSulc is recommended, if binary is not available use FS (FreeSurfer)
+
+# Requirements for this script
+#  installed versions of: FSL, Connectome Workbench (wb_command)
+#  environment: HCPPIPEDIR, FSLDIR, CARET7DIR
+
+#fslsub queue
+#QUEUE=short.q
+#top level parallelization
+
+QUEUE="long.q"
+
+#pipeline level parallelization
+#parallel mode: FSLSUB, BUILTIN, NONE
+parallel_mode=BUILTIN
+
+if [ "$parallel_mode" != FSLSUB ]; then #fsl_sub does not allow nested submissions
+if [[ "${command_line_specified_run_local}" == "TRUE" || "$QUEUE" == "" ]] ; then
+    echo "About to locally run ${HCPPIPEDIR}/PostFreeSurfer/PostFreeSurferPipelineLongLauncher.sh"
+#    #NOTE: fsl_sub without -q runs locally and captures output in files
+    queuing_command=("$FSLDIR/bin/fsl_sub")
+     QUEUE=long.q
+else
+    echo "About to use fsl_sub to queue ${HCPPIPEDIR}/FreeSurfer/PostFreeSurferPipelineLongLauncher.sh"
+    queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE")
+    QUEUE=""    
+fi
+else
+    queuing_command=""
+fi
+# This setting is for BUILTIN mode. Set to -1 to auto-detect the # of CPU cores on the node where each per-subject job is run.
+# Note that in case when multiple subject jobs are run on the same node and are submitted 
+# in parallel by e.g. fsl_sub, it may be inefficient to have the 
+# (number of fsl_sub jobs running per node) * (BUILTIN parallelism) substantially exceed
+# the number of cores per node
+max_jobs=-1
+#max_jobs=4
+
+# Stages to run. Must be run in the following order:
+# 1. PREP-TP, 2.PREP-T, 3. POSTFS-TP1, 4. POSTFS-T, 5. POSTFS-TP2
+start_stage=PREP-TP
+end_stage=POSTFS-TP2
+
+
+function identify_timepoints
+{
+    local subject=$1
+    local tplist=""
+    local tp visit n
+
+    #build the list of timepoints
+    n=0
+    for visit in ${PossibleVisits[*]}; do
+        tp="${subject}_${visit}"
+        if [ -d "$StudyFolder/$tp" ] && ! [[ " ${ExcludeVisits[*]+${ExcludeVisits[*]}} " =~ [[:space:]]"$tp"[[:space:]] ]]; then
+             if (( n==0 )); then 
+                    tplist="$tp"
+             else
+                    tplist="$tplist@$tp"
+             fi
+        fi
+        ((n++))
+    done
+    echo $tplist
+}
+
+#iterate over all subjects.
+for i in ${!Subjects[@]}; do
+  Subject=${Subjects[i]}
+  LongitudinalTemplate=${Templates[i]}
+  Timepoint_list=(`identify_timepoints $Subject`)
+
+  echo Subject: $Subject
+  echo Template: $LongitudinalTemplate
+  echo Timepoints: $Timepoint_list
+
+  cmd=(${queuing_command[@]+"${queuing_command[@]}"} ${HCPPIPEDIR}/PostFreeSurfer/PostFreeSurferPipelineLongLauncher.sh \
+    --study-folder="$StudyFolder"                       \
+    --subject="$Subject"                                \
+    --longitudinal-template="$LongitudinalTemplate"     \
+    --sessions="$Timepoint_list"                        \
+    --parallel-mode=$parallel_mode                      \
+    --fslsub-queue=$QUEUE                               \
+    --start-stage=$start_stage                          \
+    --end-stage=$end_stage                              \
+    --t1template="$T1wTemplate"                         \
+    --t1templatebrain="$T1wTemplateBrain"               \
+    --t1template2mm="$T1wTemplate2mm"                   \
+    --t2template="$T2wTemplate"                         \
+    --t2templatebrain="$T2wTemplateBrain"               \
+    --t2template2mm="$T2wTemplate2mm"                   \
+    --templatemask="$TemplateMask"                      \
+    --template2mmmask="$Template2mmMask"                \
+    --fnirtconfig="$FNIRTConfig"                        \
+    --freesurferlabels="$FreeSurferLabels"              \
+    --surfatlasdir="$SurfaceAtlasDIR"                   \
+    --grayordinatesres="$GrayordinatesResolutions"      \
+    --grayordinatesdir="$GrayordinatesSpaceDIR"         \
+    --hiresmesh="$HighResMesh"                          \
+    --lowresmesh="$LowResMeshes"                        \
+    --subcortgraylabels="$SubcorticalGrayLabels"        \
+    --refmyelinmaps="$ReferenceMyelinMaps"              \
+    --regname="$RegName"                                \    
+    )
+    echo "Running $cmd"
+    "${cmd[@]}"
+done