PFMs

Examples/Scripts/RunPFMpipelineFullRun.sh

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+#!/bin/bash
+
+set -eu
+
+# This is an example script to run the full PFM postprocessing pipeline
+# Steps involved:
+# 1. RunPROFUMO - Run PROFUMO analysis
+# 2. PostPROFUMO - Create time courses, spectra, and maps from PFM results
+# 3. RSNRegression - Run RSN regression on PFM data for dual regression
+# 4. GroupPFMs - Generate group-level statistics and averages
+#
+# Please make sure that PROFUMO, ICA-FIX, MSMAll and MakeAverageDataset are done properly 
+# matching the input arguments before running this PFM pipeline 
+
+get_options() {
+    local scriptName=$(basename "$0")
+    local arguments=("$@")
+
+    # initialize variables
+    StudyFolder="${HOME}/data/HCPpipelines_ExampleData"
+    Subjlist="100610@102311"
+    EnvironmentScript="${HOME}/projects/HCPpipelines/Examples/Scripts/SetUpHCPPipeline.sh"
+    GroupAverageName="S1200_MSMAll7T175"
+
+    RegName="MSMAll"
+    MatlabMode=1
+    RunLocal=0
+    QUEUE="matlabparallelhigh.q"
+
+    # parse arguments
+    local index argument
+
+    for ((index = 0; index < ${#arguments[@]}; ++index))
+    do
+        argument="${arguments[index]}"
+
+        case "$argument" in
+            --StudyFolder=*)
+                StudyFolder="${argument#*=}"
+                ;;
+            --Subject=*)
+                Subjlist="${argument#*=}"
+                ;;
+            --EnvironmentScript=*)
+                EnvironmentScript="${argument#*=}"
+                ;;
+            --GroupAverageName=*)
+                GroupAverageName="${argument#*=}"
+                ;;
+            --RegName=*)
+                RegName="${argument#*=}"
+                ;;
+            --MatlabMode=*)
+                MatlabMode="${argument#*=}"
+                ;;
+            *)
+                echo "ERROR: Unrecognized Option: ${argument}"
+                exit 1
+                ;;
+        esac
+    done
+
+    # check required parameters
+    if [[ "$StudyFolder" == "" ]]
+    then
+        echo "ERROR: StudyFolder not specified"
+        exit 1
+    fi
+
+    if [[ "$Subjlist" == "" ]]
+    then
+        echo "ERROR: Subjlist not specified"
+        exit 1
+    fi
+
+    if [[ "$EnvironmentScript" == "" ]]
+    then
+        echo "ERROR: EnvironmentScript not specified"
+        exit 1
+    fi
+
+    if [[ "$GroupAverageName" == "" ]]
+    then
+        echo "ERROR: GroupAverageName not specified"
+        exit 1
+    fi
+
+    # if [[ "$RegName" == "" ]]
+    # then
+    #     echo "ERROR: RegName not specified"
+    #     exit 1
+    # fi
+
+    if [[ "$MatlabMode" == "" ]]
+    then
+        echo "ERROR: MatlabMode not specified"
+        exit 1
+    fi
+
+    # report options
+    echo "-- ${scriptName}: Specified Command-Line Options: -- Start --"
+    echo "   StudyFolder: ${StudyFolder}"
+    echo "   Subjlist: ${Subjlist}"
+    echo "   EnvironmentScript: ${EnvironmentScript}"
+    echo "   GroupAverageName: ${GroupAverageName}"
+    echo "   RegName: ${RegName}"
+    echo "   MatlabMode: ${MatlabMode}"
+    echo "-- ${scriptName}: Specified Command-Line Options: -- End --"
+}
+
+# get command line options
+get_options "$@"
+
+# set up pipeline environment variables and software
+source "${EnvironmentScript}"
+
+if ((RunLocal)) || [[ "$QUEUE" == "" ]]; then
+  echo "running locally"
+  queuing_command=("$HCPPIPEDIR"/global/scripts/captureoutput.sh)
+else
+  echo "queueing with fsl_sub to $QUEUE"
+  queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE")
+fi
+
+# Download the PROFUMO Singularity image from the following link and place it in the PFM folder, 
+# or change the path below to point to your own copy of the image
+# https://balsa.wustl.edu/myelin/download?dirName=public&filepath=profumo_v2.sif
+ProfumoSingularity="$HCPPIPEDIR/PFM/profumo_v2.sif" 
+
+# general settings
+# set the start step beginning from RunPROFUMO which is by default the first step
+StartStep="RunPROFUMO"
+StopStep="GroupPFMs"
+NumWishart="6"
+KeepWishartFiles="NO"
+
+# set how many subjects to do in parallel (local, not cluster-distributed) during RSN regression, defaults to all detected physical cores, '-1'
+parLimit=-1
+
+# general inputs
+fMRINames="rfMRI_REST1_LR@rfMRI_REST1_RL@rfMRI_REST2_LR@rfMRI_REST2_RL" 
+
+randSeed=123 # random seed for PROFUMO 
+
+OutputfMRIName="rfMRI_REST"
+# set the MR concat fMRI name, if multi-run FIX was used, leave empty for single runs
+ConcatName=""
+
+# set the output spectra size for individual projection, RunsXNumTimePoints    #subjectExpectedTimepoints="3655"
+subjectExpectedTimepoints="4800"
+
+# set temporal highpass full-width (2*sigma) used in preprocessing
+HighPass="2000"
+
+#set fMRIResolution of data, like '2','1.60' or '2.40'
+fMRIResolution="2.0"  
+
+# PFM settings for REST data
+# set the PFM dimensionality
+PFMdim="76" 
+
+PFMFolder=${StudyFolder}/$GroupAverageName/MNINonLinear/Results/${OutputfMRIName}_PFM_d${PFMdim}
+# Reference image for PROFUMO
+RefImage="${StudyFolder}/$GroupAverageName/MNINonLinear/Results/${OutputfMRIName}/${OutputfMRIName}_Atlas_MSMAll_hp${HighPass}_clean_rclean_tclean_meanvn.dscalar.nii"
+
+# set the file name component representing the preprocessing already done
+fMRIProcSTRING="hp${HighPass}_clean_rclean_tclean"
+
+# set the mesh resolution, like '32' for 32k_fs_LR
+LowResMesh="32"
+
+# Define OutputSTRING with seed designation
+OutputSTRING="${OutputfMRIName}_d${PFMdim}_${GroupAverageName}_seed${randSeed}_PFMs"
+
+# RSN regression settings
+FixLegacyBiasString="NO"
+ScaleFactor="0.01"
+
+# Volume template file
+VolumeTemplateCIFTI="${HOME}/data/HCPpipelines_ExampleData/${GroupAverageName}/MNINonLinear/${GroupAverageName}_CIFTIVolumeTemplate_${OutputfMRIName}.${fMRIResolution}.dscalar.nii"
+
+## PROFUMO settings
+ProfumoConfig="${PFMFolder}/dataLocations.json"  
+TR="0.72"
+ProfumoThreads="-1" # number of threads for PROFUMO, -1 means auto-detect physical cores
+DOFCorrection="0.5"
+CovModel="Subject"
+nStarts="5" # number of multi-start iterations for PROFUMO
+RandomSeed="$randSeed" # random seed for PROFUMO reproducibility
+# RefImage will be auto-set based on data type below
+
+# build Profumo data location json
+mkdir -p $PFMFolder
+echo '{' > $ProfumoConfig
+for Subject in $(echo $Subjlist | tr "@" "\n"); do
+    echo -e "\t\"$Subject\": {" >> $ProfumoConfig
+    for fMRIName in $(echo $fMRINames | tr "@" "\n"); do
+        runFile="${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}.dtseries.nii"
+        if [[ -e $runFile ]]; then
+            echo -e "\t\t\"$fMRIName\": \"$runFile\"," >> $ProfumoConfig
+        fi
+    done
+    perl -pi -e 'if (eof) { s/,$// }' $ProfumoConfig  # remove trailing comma
+    echo -e "\t}," >> $ProfumoConfig
+done
+perl -pi -e 'if (eof) { s/,$// }' $ProfumoConfig  # remove trailing comma
+echo "}" >> $ProfumoConfig
+
+# PFM pipeline execution
+echo "Starting PFM postprocessing pipeline"
+echo "Data type: ${OutputfMRIName}"
+echo "PFM dimension: ${PFMdim}"
+
+"${queuing_command[@]}" "$HCPPIPEDIR"/PFM/PFMPipeline.sh \
+                                --study-folder="$StudyFolder" \
+                                --subject-list="$Subjlist" \
+                                --fmri-names="$fMRINames" \
+                                --output-fmri-name="$OutputfMRIName" \
+                                --output-string="$OutputSTRING" \
+                                --proc-string="$fMRIProcSTRING" \
+                                --group-average-name="$GroupAverageName" \
+                                --pfm-dimension="$PFMdim" \
+                                --pfm-folder="$PFMFolder" \
+                                --surf-reg-name="$RegName" \
+                                --concat-name="$ConcatName" \
+                                --low-res-mesh="$LowResMesh" \
+                                --runs-timepoints="$subjectExpectedTimepoints" \
+                                --fix-legacy-bias="$FixLegacyBiasString" \
+                                --num-wishart="$NumWishart"\
+                                --scale-factor="$ScaleFactor" \
+                                --starting-step="$StartStep" \
+                                --stop-after-step="$StopStep" \
+                                --parallel-limit="$parLimit" \
+                                --matlab-run-mode="$MatlabMode" \
+                                --profumo-config="$ProfumoConfig" \
+                                --profumo-singularity="$ProfumoSingularity" \
+                                --profumo-tr="$TR" \
+                                --keep-wishart-files="$KeepWishartFiles" \
+                                --profumo-threads="$ProfumoThreads" \
+                                --profumo-dof-correction="$DOFCorrection" \
+                                --profumo-cov-model="$CovModel" \
+                                --profumo-multi-start-iterations="$nStarts" \
+                                --profumo-random-seed="$RandomSeed" \
+                                --ref-image="$RefImage" \
+                                --volume-template-file="$VolumeTemplateCIFTI"
+
+echo "PFM pipeline submitted successfully!"
+

PFM/.gitignore

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+*.sif