diff --git a/Examples/Scripts/RunPFMpipelineFullRun.sh b/Examples/Scripts/RunPFMpipelineFullRun.sh
new file mode 100755
index 000000000..44ee1b93a
--- /dev/null
+++ b/Examples/Scripts/RunPFMpipelineFullRun.sh
@@ -0,0 +1,248 @@
+#!/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!"
+
diff --git a/PFM/.gitignore b/PFM/.gitignore
new file mode 100644
index 000000000..6e91d7ef0
--- /dev/null
+++ b/PFM/.gitignore
@@ -0,0 +1 @@
+*.sif
diff --git a/PFM/PFMPipeline.sh b/PFM/PFMPipeline.sh
new file mode 100755
index 000000000..4c4700ccf
--- /dev/null
+++ b/PFM/PFMPipeline.sh
@@ -0,0 +1,516 @@
+#!/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" "$@"
+source "$HCPPIPEDIR/global/scripts/tempfiles.shlib" "$@"
+source "$HCPPIPEDIR/global/scripts/parallel.shlib" "$@"
+
+g_matlab_default_mode=1
+
+# add steps to this array and in the switch cases below
+pipelineSteps=(RunPROFUMO PostPROFUMO RSNRegression GroupPFMs)
+defaultStart="${pipelineSteps[0]}"
+defaultStopAfter="${pipelineSteps[${#pipelineSteps[@]} - 1]}"
+stepsText="$(IFS=$'\n'; echo "${pipelineSteps[*]}")"
+
+#description to use in usage
+opts_SetScriptDescription "implements complete PFM pipeline with four main steps: Run PROFUMO, Post-PROFUMO, RSN Regression, and Group PFM processing"
+
+#mandatory parameters
+opts_AddMandatory '--study-folder' 'StudyFolder' 'path' "folder that contains all subjects"
+opts_AddMandatory '--subject-list' 'SubjlistRaw' '100206@100307...' "list of subject IDs separated by @s"
+opts_AddMandatory '--fmri-names' 'fMRINames' 'rfMRI_REST1_LR@rfMRI_REST1_RL...' "list of fmri run names separated by @s"
+opts_AddMandatory '--output-fmri-name' 'OutputfMRIName' 'rfMRI_REST' "name to use for PFM pipeline outputs"
+opts_AddMandatory '--output-string' 'OutputSTRING' 'string' "output string for individual subject files (typically includes dimension, group name, and seed)"
+opts_AddMandatory '--proc-string' 'fMRIProcSTRING' 'string' "file name component representing the preprocessing already done, e.g. '_Atlas_MSMAll_hp0_clean_tclean'"
+opts_AddMandatory '--group-average-name' 'GroupAverageName' 'string' 'name to use for the group output folder'
+opts_AddMandatory '--pfm-dimension' 'PFMdim' 'integer' "PFM dimensionality (e.g., 76, 92, 65)"
+opts_AddMandatory '--pfm-folder' 'PFMFolder' 'path' "path to PFM results folder containing Results.ppp"
+opts_AddMandatory '--surf-reg-name' 'RegName' 'MSMAll' "the registration string corresponding to the input files"
+opts_AddMandatory '--profumo-config' 'ProfumoConfig' 'path' "path to PROFUMO JSON configuration file"
+opts_AddMandatory '--profumo-tr' 'TR' "seconds" "repetition time for PROFUMO analysis"
+opts_AddMandatory '--ref-image' 'RefImage' 'path' "reference image for PROFUMO postprocessing"
+opts_AddMandatory '--runs-timepoints' 'RunsXNumTimePoints' "total timepoints across runs" "total timepoints across runs"
+opts_AddMandatory '--concat-name' 'ConcatName' "concatenated fMRI name if using multi-run data" ''
+opts_AddMandatory '--volume-template-file' 'VolumeTemplateFile' "volume template file path" ''
+
+#PROFUMO specific parameters
+opts_AddOptional '--profumo-threads' 'ProfumoThreads' 'integer' "number of threads for PROFUMO" '-1'
+opts_AddOptional '--profumo-dof-correction' 'DOFCorrection' 'float' "DOF correction for PROFUMO" '0.5'
+opts_AddOptional '--profumo-cov-model' 'CovModel' 'string' "covariance model for PROFUMO" 'Subject'
+opts_AddOptional '--profumo-singularity' 'ProfumoSingularity' 'path' "path to PROFUMO singularity container"
+opts_AddOptional '--profumo-random-seed' 'RandomSeed' 'integer' "random seed for PROFUMO" '123'
+opts_AddOptional '--profumo-multi-start-iterations' 'MultiStartIterations' 'integer' "number of iterations of group-level spatial decomposition before inferring full model" '5'
+opts_AddOptional '--profumo-initial-maps' 'InitialMaps' 'path' "file to initialise the decomposition based on spatial maps"
+opts_AddOptional '--profumo-load-sequentially' 'LoadSequentially' 'YES or NO' "load data sequentially in PROFUMO (useful for memory management)" 'YES'
+opts_AddOptional '--num-wishart' 'NumWishart' 'integer' "number of Wishart filter iterations for prefiltering (0 to skip)" '0'
+
+# Post-Wishart filter specific parameters (only used if --num-wishart > 0)
+opts_AddOptional '--keep-wishart-files' 'KeepWishartFiles' 'YES or NO' "keep Wishart-filtered files after PROFUMO instead of deleting (default NO)" 'NO'
+opts_AddOptional '--variance-normalization' 'VarNorm' 'YES or NO' "Variance normalize data before PROFUMO (default YES)" 'YES'
+opts_AddOptional '--weight-vertex-areas' 'VAweight' 'YES or NO' "Weight data by vertex areas before PROFUMO (default YES)" 'YES'
+
+#optional parameters
+opts_AddOptional '--low-res-mesh' 'LowResMesh' 'string' "mesh resolution, like '32' for 32k_fs_LR" '32'
+
+#RSN regression specific parameters
+opts_AddOptional '--fix-legacy-bias' 'FixLegacyBias' 'YES or NO' 'whether the input data used legacy bias correction' 'NO'
+opts_AddOptional '--scale-factor' 'ScaleFactor' 'float' 'scale factor for RSN regression' '0.01'
+
+
+#general settings
+opts_AddOptional '--starting-step' 'startStep' 'step' "what step to start processing at, one of:
+$stepsText" "$defaultStart"
+opts_AddOptional '--stop-after-step' 'stopAfterStep' 'step' "what step to stop processing after, same valid values as --starting-step" "$defaultStopAfter"
+opts_AddOptional '--parallel-limit' 'parLimit' 'integer' "set how many subjects to do in parallel during RSN regression, defaults to all detected physical cores" '-1'
+opts_AddOptional '--matlab-run-mode' 'MatlabMode' '0, 1, or 2' "defaults to $g_matlab_default_mode
+0 = compiled MATLAB
+1 = interpreted MATLAB
+2 = Octave" "$g_matlab_default_mode"
+
+opts_ParseArguments "$@"
+
+if ((pipedirguessed))
+then
+    log_Err_Abort "HCPPIPEDIR is not set, you must first source your edited copy of Examples/Scripts/SetUpHCPPipeline.sh"
+fi
+
+#display the parsed/default values
+opts_ShowValues
+
+if [[ "$ProfumoThreads" == "-1" ]]; then
+    ProfumoThreads=$(par_numphys)
+fi  
+
+#processing code goes here
+IFS='@' read -a Subjlist <<<"$SubjlistRaw"
+IFS='@' read -a fMRINamesArray <<<"$fMRINames"
+
+FixLegacyBiasBool=$(opts_StringToBool "$FixLegacyBias")
+KeepWishartBool=$(opts_StringToBool "$KeepWishartFiles")
+VarNormBool=$(opts_StringToBool "$VarNorm")
+VAweightBool=$(opts_StringToBool "$VAweight")
+
+if ! [[ "$parLimit" == "-1" || "$parLimit" =~ [1-9][0-9]* ]]
+then
+    log_Err_Abort "--parallel-limit must be a positive integer or -1, provided value: '$parLimit'"
+fi
+
+function stepNameToInd()
+{
+    for ((i = 0; i < ${#pipelineSteps[@]}; ++i))
+    do
+        if [[ "$1" == "${pipelineSteps[i]}" ]]
+        then
+            echo "$i"
+            return
+        fi
+    done
+    log_Err_Abort "unrecognized step name: '$1'"
+}
+
+
+
+startInd=$(stepNameToInd "$startStep")
+stopAfterInd=$(stepNameToInd "$stopAfterStep")
+
+if ((startInd > stopAfterInd))
+then
+    log_Err_Abort "starting step '$startStep' must not be after the stopping step '$stopAfterStep'"
+fi
+
+RegString=""
+if [[ "$RegName" != "" ]]
+then
+    RegString="_$RegName"
+fi
+
+
+for ((stepInd = startInd; stepInd <= stopAfterInd; ++stepInd))
+do
+    stepName="${pipelineSteps[stepInd]}"
+    case "$stepName" in
+        (RunPROFUMO)
+            log_Msg "Running PROFUMO analysis step"
+            
+            # Validate required PROFUMO parameters
+            if [[ "$ProfumoConfig" == "" ]]
+            then
+                log_Err_Abort "PROFUMO config file must be specified with --profumo-config"
+            fi
+            if [[ "$ProfumoSingularity" == "" ]]
+            then
+                log_Err_Abort "PROFUMO singularity container must be specified with --profumo-singularity"
+            fi
+            if [[ "$RefImage" == "" ]]
+            then
+                log_Err_Abort "Reference image must be specified with --ref-image"
+            fi
+            
+            ProfumoConfigToUse="${ProfumoConfig}"
+            if [[ "$NumWishart" -gt 0 ]]
+            then
+                WFDir="${PFMFolder}/WishartFilter_WF${NumWishart}"
+                # Check if WF files already exist
+                wfComplete=true
+                for Subject in "${Subjlist[@]}"
+                do
+                    for fMRIName in "${fMRINamesArray[@]}"
+                    do
+                        inputFile="${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}.dtseries.nii"
+                        wfFile="${WFDir}/${Subject}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}_WF.dtseries.nii"
+                        if [[ -f "$inputFile" ]] && [[ ! -f "$wfFile" ]]
+                        then
+                            wfComplete=false
+                            break 2
+                        fi
+                    done
+                done
+                
+                if $wfComplete && [[ $KeepWishartBool == 1 ]]; then
+                    log_Msg "WF files already exist in ${WFDir}"
+                else
+                    log_Msg "Running Wishart filtering with ${NumWishart} iterations"
+                    for Subject in "${Subjlist[@]}"
+                    do
+                        mkdir -p "${WFDir}/${Subject}"
+                        
+                        if [[ "$ConcatName" != "" ]] # multi_run data
+                        then
+                            # Use already concatenated file
+                            concatFile="${StudyFolder}/${Subject}/MNINonLinear/Results/${ConcatName}/${ConcatName}_Atlas${RegString}_${fMRIProcSTRING}.dtseries.nii"
+                            clean_VN="${StudyFolder}/${Subject}/MNINonLinear/Results/${ConcatName}/${ConcatName}_Atlas${RegString}_${fMRIProcSTRING}_vn.dscalar.nii"
+                            concatOutFile="${WFDir}/${Subject}/${ConcatName}_Atlas${RegString}_${fMRIProcSTRING}_WF.dtseries.nii"
+                            if [[ -f "$concatFile" ]]
+                            then
+                                log_Msg "Applying Wishart filter to concat file for subject $Subject"
+                                "$HCPPIPEDIR"/PFM/scripts/ApplyWFProfumo.sh \
+                                    --input="$concatFile" \
+                                    --output="$concatOutFile" \
+                                    --num-wishart="$NumWishart" \
+                                    --matlab-run-mode="$MatlabMode"
+
+                                if [[ "$VAweightBool" == 1 ]]; then
+                                    # create temporary VA_norm cifti with volume grayordinates filled with ones areas for weighting 
+                                    VAnorm=${StudyFolder}/${Subject}/T1w/fsaverage_LR${LowResMesh}k/${Subject}.midthickness${RegString}_va_norm.${LowResMesh}k_fs_LR.dscalar.nii
+                                    tempfiles_create "tmp_VAgray_XXXXXX.dscalar.nii" tmp_VAgray_file
+                                    tempfiles_create "tmp_jnk_XXXXXX.nii.gz" tmp_jnk_file
+                                    tempfiles_create "tmp_roi_XXXXXX.nii.gz" tmp_roi_file
+                                    wb_command -cifti-separate "${concatOutFile}" COLUMN -volume-all "$tmp_jnk_file" -roi "$tmp_roi_file" -crop
+                                    wb_command -cifti-create-dense-from-template "${concatOutFile}" "$tmp_VAgray_file" -cifti "$VAnorm" -volume-all "$tmp_roi_file" -from-cropped
+                                fi
+                                                                                  
+                                # Split back into individual runs and restore means
+                                cumTP=0
+                                for fMRIName in "${fMRINamesArray[@]}"
+                                do
+                                    origFile="${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}.dtseries.nii"
+                                    if [[ -f "$origFile" ]]
+                                    then
+                                        nTP=$(wb_command -file-information "$origFile" -only-number-of-maps)
+                                        startIdx=$((cumTP + 1))
+                                        endIdx=$((cumTP + nTP))
+                                        outFile="${WFDir}/${Subject}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}_WF.dtseries.nii"
+                                        wb_command -cifti-merge "$outFile" -direction ROW -cifti "$concatOutFile" -index "$startIdx" -up-to "$endIdx" # naive splitting
+                                        
+                                        ## The concatenated timeseries are intensity normalized and differences in unstructured noise variance between runs and the means have been removed.
+                                        #  For model-free analyses (i.e., not task-GLM) that prefer single runs, it is best to simply deconcatenate the runs.  
+                                        #  If variance normalization is desired, use the same _clean_vn file from the concatenated folder for each run, rather than the original _vn files, 
+                                        #  which may cause extreme values in areas of little or no signal and require more complex handling.
+                                        if [[ "$VarNormBool" == 1 ]];then
+                                            log_Msg "Normalizing variance"
+                                            wb_command -cifti-math "(TCS / clean_VN)" ${outFile} \
+                                                -var TCS ${outFile} \
+                                                -var clean_VN ${clean_VN} -select 1 1 -repeat
+                                        fi
+
+                                        if [[ "$VAweightBool" == 1 ]];then
+                                            log_Msg "Weighting data by average vertex areas"
+                                            wb_command -cifti-math "(TCS * VA)" ${outFile} \
+                                                -var TCS ${outFile} \
+                                                -var VA ${tmp_VAgray_file} -select 1 1 -repeat
+                                        fi
+
+                                        cumTP=$endIdx
+                                    fi
+                                done
+                            fi
+                        else # single run data
+                            echo ToDO
+                            # No concat file not supplied so create a temporary one for Wishart filtering
+                            # demeanVNarray=()
+                            # vnScalarArray=()
+                            # for fMRIName in "${fMRINamesArray[@]}"
+                            # do
+                            #     inputFile="${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}.dtseries.nii"
+                            #     vnScalarFile="${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}_vn.dscalar.nii"
+                            #     meanFile="${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_mean.dscalar.nii"
+                            #     outputFile="${WFDir}/${Subject}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}_WF.dtseries.nii"
+              
+                            #     # demean and variance normalize runs
+                            #     wb_command -cifti-math "(TCS - MEAN) / VN" "$outputFile" -var TCS "$inputFile" -var MEAN "$meanFile" -var VN "$vnScalarFile" -select 1 1 -repeat
+                            #     demeanVNarray+=("$outputFile")
+                            #     vnScalarArray+=("$vnScalarFile")
+                            # done
+
+                            # # concatenate the demeaned+VN files
+                            # concatOutFile="${WFDir}/${Subject}/CONCAT_Atlas${RegString}_${fMRIProcSTRING}_WF.dtseries.nii"
+                            # wb_shortcuts -cifti-concatenate "${concatOutFile}" "${demeanVNarray[*]}"
+                            
+
+                            # log_Msg "Applying Wishart filter for subject $Subject"
+                            # "$HCPPIPEDIR"/PFM/scripts/ApplyWFProfumo.sh \
+                            #     --input="$concatOutFile" \
+                            #     --output="$concatOutFile" \
+                            #     --num-wishart="$NumWishart" \
+                            #     --matlab-run-mode="$MatlabMode"
+
+                            # # deconcatenate the Wishart filtered data back into individual runs
+                            # # (each run has its own VN file, so un-VN with each separately)
+                            # cumTP=0
+                            # for fMRIName in "${fMRINamesArray[@]}"
+                            # do
+                            #     origFile="${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}.dtseries.nii"
+                            #     vnScalarFile="${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}_vn.dscalar.nii"
+                            #     meanFile="${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_mean.dscalar.nii"
+                            #     if [[ -f "$origFile" ]]
+                            #     then
+                            #         nTP=$(wb_command -file-information "$origFile" -only-number-of-maps)
+                            #         startIdx=$((cumTP + 1))
+                            #         endIdx=$((cumTP + nTP))
+                            #         outFile="${WFDir}/${Subject}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}_WF.dtseries.nii"
+                            #         wb_command -cifti-merge "$outFile" -direction ROW -cifti "$concatOutFile" -index "$startIdx" -up-to "$endIdx"
+                                    
+                            #         # un-variance normalize and un-demean each post-WF run
+                            #         wb_command -cifti-math "(TCS / VN) + MEAN" "$outFile" -var TCS "$outFile" -var MEAN "$meanFile" -var VN "$vnScalarFile" -select 1 1 -repeat
+                                  
+                            #         cumTP=$endIdx
+                            #     fi
+                            # done
+                        fi
+                    done
+                fi
+                
+                # Build JSON pointing at WF files
+                ProfumoConfigToUse="${WFDir}/wishart_dataLocations.json"
+                echo '{' > "$ProfumoConfigToUse"
+                for Subject in "${Subjlist[@]}"
+                do
+                    echo -e "\t\"$Subject\": {" >> "$ProfumoConfigToUse"
+                    for fMRIName in "${fMRINamesArray[@]}"
+                    do
+                        WFFile="${WFDir}/${Subject}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}_WF.dtseries.nii"
+                        if [[ -f "$WFFile" ]]
+                        then
+                            echo -e "\t\t\"$fMRIName\": \"$WFFile\"," >> "$ProfumoConfigToUse"
+                        fi
+                    done
+                    perl -pi -e 'if (eof) { s/,$// }' "$ProfumoConfigToUse"
+                    echo -e "\t}," >> "$ProfumoConfigToUse"
+                done
+                perl -pi -e 'if (eof) { s/,$// }' "$ProfumoConfigToUse"
+                echo "}" >> "$ProfumoConfigToUse"
+                log_Msg "WF complete"
+            fi
+
+
+            # Set up PROFUMO paths
+            PFM_PATH="${PFMFolder}/Analysis.pfm"
+            RESULTS_PATH="${PFMFolder}/Results.ppp"
+            REAL_REF_IMAGE=$(readlink -f "${RefImage}")
+            
+            # Calculate low rank data parameter
+            LowRankData=$((PFMdim * 5))
+            
+            # if PFM output directory exists, clear it (except dataLocations.json) because PROFUMO otherwise creates "+" files instead of overwriting
+            if [[ -d "${PFMFolder}" ]]
+            then
+                log_Warn "PFM output folder ${PFMFolder} already exists, clearing contents"
+                find "${PFMFolder}" -mindepth 1 -not -name "dataLocations.json" -not -name ".*" -not -path "*/WishartFilter_WF*" -delete 2>/dev/null || true
+                # ignore errors due to nfs silly renamed files, or similar
+            fi
+
+            # Build optional initialMaps argument
+            InitialMapsArg=""
+            if [[ -n "${InitialMaps}" && -f "${InitialMaps}" ]]
+            then
+                InitialMapsArg="--initialMaps ${InitialMaps}"
+            fi
+            
+            # Build optional loadSequentially argument
+            LoadSequentiallyArg=""
+            LoadSequentiallyBool=$(opts_StringToBool "$LoadSequentially")
+            if ((LoadSequentiallyBool))
+            then
+                LoadSequentiallyArg="--loadSequentially"
+            fi
+            
+            # files were written with an older version of cifti-matlab with 8-byte instead of 16-byte alignment. 
+            if [[ "${NumWishart}" -eq 0 ]]
+            then
+                cat "${ProfumoConfig}" | \
+                    while IFS= read -r line; do
+                        if [[ "$line" != *'.nii"'* ]]; then continue;fi # Only process lines that contain .nii"
+                        filePath=$(echo "$line" | sed -E 's/^[[:space:]]*"[^"]*"[[:space:]]*:[[:space:]]*"([^"]*)".*/\1/')
+                        wb_command -file-convert -cifti-version-convert "$filePath" 2 "$filePath"
+                    done           
+            fi
+
+            # log_Msg "Running PROFUMO decomposition with dimension ${PFMdim}"
+            cmd=(apptainer exec --bind $(dirname "${StudyFolder}") \
+                --env PROFUMODIR=/opt/profumo \
+                --env PYTHONNOUSERSITE=1 \
+                "${ProfumoSingularity}" \
+                /opt/profumo/C++/PROFUMO "${ProfumoConfigToUse}" \
+                "${PFMdim}" "${PFM_PATH}" \
+                --useHRF "${TR}" --covModel "${CovModel}" --dofCorrection "${DOFCorrection}" \
+                --nThreads "${ProfumoThreads}" --lowRankData "${LowRankData}" --randomSeed "${RandomSeed}" \
+                --multiStartIterations "${MultiStartIterations}" ${LoadSequentiallyArg} ${InitialMapsArg})
+            log_Msg "running command: ${cmd[*]}"
+            "${cmd[@]}"
+            
+            #Cleanup WF files
+            if [[ "$NumWishart" -gt 0 ]]
+            then
+                if ((KeepWishartBool))
+                then
+                    log_Msg "Keeping Wishart filtered files in ${WFDir}"
+                else
+                    log_Msg "Cleaning up Wishart filtered files"
+                    rm -rf "${WFDir}"  2>/dev/null || true # ignore errors due to nfs silly renamed files, or similar
+                fi
+            fi          
+            ;;
+            
+        (PostPROFUMO)
+            log_Msg "Running PROFUMO postprocessing"
+            PFM_PATH="${PFMFolder}/Analysis.pfm"
+            RESULTS_PATH="${PFMFolder}/Results.ppp"
+            REAL_REF_IMAGE=$(readlink -f "${RefImage}")
+
+            # Remove any existing Results.ppp directory 
+            # so postprocess_results.py writes fresh output to Results.ppp
+            if [[ -d "${PFMFolder}/Results.ppp" ]]
+            then
+                log_Warn "Results.ppp folder ${PFMFolder}/Results.ppp already exists, clearing before postprocessing"
+                rm -rf "${PFMFolder}"/Results.ppp 2>/dev/null || true # ignore errors due to nfs silly renamed files, or similar
+            fi
+
+            cmd=(apptainer exec --bind $(dirname "${StudyFolder}") \
+                --env PROFUMODIR=/opt/profumo \
+                --env PYTHONNOUSERSITE=1 \
+                "${ProfumoSingularity}" \
+                /opt/fsl/fslpython/envs/profumo/bin/python3 /opt/profumo/Python/postprocess_results.py \
+                --web-report \
+                "${PFM_PATH}" \
+                "${RESULTS_PATH}" \
+                "${REAL_REF_IMAGE}")
+            log_Msg "Running command: ${cmd[*]}"
+            "${cmd[@]}"
+
+            log_Msg "Running PostPROFUMO step"
+            "$HCPPIPEDIR"/PFM/scripts/PostPROFUMO.sh \
+                --study-folder="$StudyFolder" \
+                --subject-list="$SubjlistRaw" \
+                --fmri-names="$fMRINames" \
+                --concat-name="$ConcatName" \
+                --proc-string="_Atlas${RegString}_${fMRIProcSTRING}" \
+                --output-fmri-name="$OutputfMRIName" \
+                --output-string="$OutputSTRING" \
+                --surf-reg-name="$RegName" \
+                --low-res-mesh="$LowResMesh" \
+                --profumo-tr="$TR" \
+                --pfm-folder="$PFMFolder" \
+                --variance-normalize="$VarNorm" \
+                --weight-vertex-areas="$VAweight" \
+                --matlab-run-mode="$MatlabMode"
+
+            ;;
+        (RSNRegression)
+            log_Msg "Running RSNRegression step"
+            
+            # Set up template paths            
+            for Subject in "${Subjlist[@]}"
+            do
+                if [[ "$ConcatName" != "" ]]
+                then
+                    fMRINamesForSub="${ConcatName}"
+                else 
+                    # Build list of existing fMRI files for this subject (same logic as your example)
+                    fMRINamesForSub=""
+                    for fMRIName in "${fMRINamesArray[@]}"
+                    do
+                        if [[ -f "${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas${RegString}_${fMRIProcSTRING}.dtseries.nii" ]]
+                        then
+                            if [[ "$fMRINamesForSub" != "" ]]
+                            then
+                                fMRINamesForSub="${fMRINamesForSub}@${fMRIName}"
+                            else
+                                fMRINamesForSub="${fMRIName}"
+                            fi
+                        fi
+                    done
+                fi
+
+                if [[ "$fMRINamesForSub" == "" ]]
+                then
+                    log_Warn "No valid fMRI runs found for subject $Subject, skipping"
+                    continue
+                fi
+                
+                # Set maps for dual regression
+                GroupMaps="${PFMFolder}/Results.ppp/Maps/Group.dscalar.nii"
+                
+                # Build RSN regression command 
+                rsn_cmd=("$HCPPIPEDIR"/global/scripts/RSNregression.sh
+                    --study-folder="$StudyFolder"
+                    --subject="$Subject"
+                    --subject-timeseries="$fMRINamesForSub" # "$fMRINamesForSub"
+                    --surf-reg-name="$RegName"
+                    --low-res="$LowResMesh"
+                    --proc-string="_$fMRIProcSTRING"
+                    --method="dual"
+                    --output-string="$OutputSTRING"
+                    --output-spectra="$RunsXNumTimePoints"
+                    --volume-template-cifti="$VolumeTemplateFile"
+                    --output-z=1
+                    --fix-legacy-bias="$FixLegacyBias"
+                    --scale-factor="$ScaleFactor"
+                    --group-maps="$GroupMaps"
+                )
+                
+                # Queue parallel job
+                par_addjob "${rsn_cmd[@]}"
+            done
+            
+            # Run the jobs
+            par_runjobs "$parLimit"
+            ;;
+        (GroupPFMs)
+            log_Msg "Running GroupPFMs step"
+            "$HCPPIPEDIR"/PFM/scripts/GroupPFMs.sh \
+                --study-folder="$StudyFolder" \
+                --subject-list="$SubjlistRaw" \
+                --pfm-dimension="$PFMdim" \
+                --output-string="$OutputSTRING" \
+                --surf-reg-name="$RegName" \
+                --low-res-mesh="$LowResMesh" \
+                --runs-timepoints="$RunsXNumTimePoints" \
+                --pfm-folder="$PFMFolder" \
+                --matlab-run-mode="$MatlabMode"
+            ;;
+        (*) #NOTE: this case MUST be last
+            log_Err_Abort "internal error: unimplemented pipeline step '$stepName'"
+            ;;
+    esac
+    log_Msg "step $stepName complete"
+done
diff --git a/PFM/scripts/ApplyWFProfumo.m b/PFM/scripts/ApplyWFProfumo.m
new file mode 100644
index 000000000..30a3b4028
--- /dev/null
+++ b/PFM/scripts/ApplyWFProfumo.m
@@ -0,0 +1,7 @@
+function ApplyWFProfumo(inputFile, outputFile, numWisharts)
+  numWisharts = str2double(numWisharts);
+  cii = ciftiopen(strtrim(inputFile), 'wb_command');
+  Out = icaDim(cii.cdata, 0, 1, -1, numWisharts);
+  cii.cdata = Out.data;
+  ciftisave(cii, strtrim(outputFile), 'wb_command');
+end
\ No newline at end of file
diff --git a/PFM/scripts/ApplyWFProfumo.sh b/PFM/scripts/ApplyWFProfumo.sh
new file mode 100755
index 000000000..8b860f221
--- /dev/null
+++ b/PFM/scripts/ApplyWFProfumo.sh
@@ -0,0 +1,84 @@
+#!/bin/bash
+set -eu
+
+pipedirguessed=0
+if [[ "${HCPPIPEDIR:-}" == "" ]]
+then
+    pipedirguessed=1
+    export HCPPIPEDIR="$(dirname -- "$0")/../.."
+fi
+
+source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
+source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
+g_matlab_default_mode=1
+
+opts_SetScriptDescription "applies Wishart filter to CIFTI dtseries files for PROFUMO"
+
+opts_AddMandatory '--input' 'inputFile' 'file' "comma-separated list of input dtseries files"
+opts_AddMandatory '--output' 'outputFile' 'file' "comma-separated list of output wishart-filtered dtseries files"
+opts_AddMandatory '--num-wishart' 'numWisharts' 'integer' "number of Wishart distributions to fit"
+opts_AddOptional '--matlab-run-mode' 'MatlabMode' '0, 1, or 2' "defaults to $g_matlab_default_mode
+
+0 = compiled MATLAB
+1 = interpreted MATLAB
+2 = Octave" "$g_matlab_default_mode"
+
+opts_ParseArguments "$@"
+
+if ((pipedirguessed))
+then
+    log_Err_Abort "HCPPIPEDIR is not set, you must first source your edited copy of Examples/Scripts/SetUpHCPPipeline.sh"
+fi
+
+opts_ShowValues
+
+case "$MatlabMode" in
+    (0)
+        if [[ "${MATLAB_COMPILER_RUNTIME:-}" == "" ]]
+        then
+            log_Err_Abort "to use compiled matlab, you must set and export the variable MATLAB_COMPILER_RUNTIME"
+        fi
+        ;;
+    (1)
+        matlab_interpreter=(matlab -nodisplay -nosplash)
+        ;;
+    (2)
+        matlab_interpreter=(octave-cli -q --no-window-system)
+        ;;
+    (*)
+        log_Err_Abort "unrecognized matlab mode '$MatlabMode', use 0, 1, or 2"
+        ;;
+esac
+
+this_script_dir=$(dirname "$0")
+
+matlab_argarray=("$inputFile" "$outputFile" "$numWisharts")
+
+case "$MatlabMode" in
+    (0)
+        matlab_cmd=("$this_script_dir/Compiled_WishartFilter/run_WishartFilter.sh" "$MATLAB_COMPILER_RUNTIME" "${matlab_argarray[@]}")
+        log_Msg "running compiled matlab command: ${matlab_cmd[*]}"
+        "${matlab_cmd[@]}"
+        ;;
+    (1 | 2)
+        matlab_args=""
+        for thisarg in "${matlab_argarray[@]}"
+        do
+            if [[ "$matlab_args" != "" ]]
+            then
+                matlab_args+=", "
+            fi
+            matlab_args+="'$thisarg'"
+        done
+        matlabcode="
+            addpath('$HCPPIPEDIR/global/matlab/icaDim');
+            addpath('$HCPPIPEDIR/global/matlab');
+            addpath('$this_script_dir');
+            addpath('$HCPCIFTIRWDIR');
+            ApplyWFProfumo($matlab_args);"
+
+        log_Msg "running matlab code: $matlabcode"
+        "${matlab_interpreter[@]}" <<<"$matlabcode"
+        echo
+        ;;
+esac
\ No newline at end of file
diff --git a/PFM/scripts/GroupPFMs.m b/PFM/scripts/GroupPFMs.m
new file mode 100755
index 000000000..5f1950188
--- /dev/null
+++ b/PFM/scripts/GroupPFMs.m
@@ -0,0 +1,126 @@
+function GroupPFMs(StudyFolder, SubjlistRaw, PFMdim, OutputSTRING, RegName, LowResMesh, RunsXNumTimePoints, PFMFolder)
+% GroupPFMs(StudyFolder, SubjlistRaw, PFMdim, OutputSTRING, RegName, LowResMesh, RunsXNumTimePoints, PFMFolder)
+% This function aggregates individual subject PFM results and computes
+% group-level time course masks, spectra, maps, and statistics.
+%
+% Inputs:
+%   StudyFolder - Path to the study directory
+%   SubjlistRaw - Subject list as @ separated string
+%   PFMdim - PFM dimensionality
+%   OutputSTRING - Output string for files
+%   RegName - Registration string (e.g., '_MSMAll')
+%   LowResMesh - Mesh resolution (e.g., '32' for 32k_fs_LR)
+%   RunsXNumTimePoints - Total expected timepoints across runs
+%   PFMFolder - Output folder for group-level results
+
+%% Initialize parameters
+wbcommand = 'wb_command';
+
+%% Parse input arguments
+subjList = regexp(SubjlistRaw,'@','split');
+nS = numel(subjList);
+RunsXNumTimePoints = str2double(RunsXNumTimePoints);
+PFMdim = str2double(PFMdim);
+if nargin < 8; error('All arguments are required.'); end % Validate all inputs
+
+%% Preallocate arrays for group concatenation
+% TCSMask: binary mask indicating valid timepoints per subject
+% TCSAll: concatenated time courses across subjects
+% spectra, PFMmaps, PFMvolMaps: accumulators for group averages
+[TCSMask, TCSAll] = deal(zeros(PFMdim, RunsXNumTimePoints, nS, 'single'));
+[spectra, PFMmaps, PFMvolMaps] = deal([]);
+
+%% Load and accumulate individual subject results
+for iS = 1:nS
+  subj = subjList{iS};
+  subjDir = [StudyFolder '/' subj '/MNINonLinear/fsaverage_LR' LowResMesh 'k'];
+  fprintf('Processing %s ... \n', subj);
+  
+  %% Load individual PFM results from standard subject locations
+  % Load spatial maps, volume maps, time courses, and power spectra
+  PFMMapsSub = ciftiopen([subjDir '/' subj '.' OutputSTRING '_DR' RegName '.' LowResMesh 'k_fs_LR.dscalar.nii'], wbcommand);
+  PFMVolMapsSub = ciftiopen([subjDir '/' subj '.' OutputSTRING '_DR' RegName '_vol.' LowResMesh 'k_fs_LR.dscalar.nii'], wbcommand);
+  TCSSub = ciftiopen([subjDir '/' subj '.' OutputSTRING '_DR' RegName '_ts.' LowResMesh 'k_fs_LR.sdseries.nii'], wbcommand);
+  SpectraSub = ciftiopen([subjDir '/' subj '.' OutputSTRING '_DR' RegName '_spectra.' LowResMesh 'k_fs_LR.sdseries.nii'], wbcommand);
+
+  %% Clean up NaNs and Infs in volume maps
+  % Replace invalid values with zeros to prevent propagation to group statistics
+  infMask = isinf(PFMVolMapsSub.cdata);
+  nanMask = isnan(PFMVolMapsSub.cdata);
+  if any(infMask, 'all')
+    warning('Found Infs in PFM VolMaps for subject %s. Replacing with zeros.\n', subj);
+    PFMVolMapsSub.cdata(isinf(PFMVolMapsSub.cdata)) = 0;
+  end
+  if any(nanMask, 'all')
+    warning('Found NaNs in PFM VolMaps for subject %s. Replacing with zeros.\n', subj);
+    PFMVolMapsSub.cdata(isnan(PFMVolMapsSub.cdata)) = 0;
+  end
+
+  %% Store subject time course in concatenated array
+  TCSAll(1:size(TCSSub.cdata, 1), 1:size(TCSSub.cdata, 2), iS) = TCSSub.cdata;
+
+  %% Accumulate spectra and maps for group averaging
+  % Only accumulate if subject has expected number of timepoints
+  if size(TCSSub.cdata, 2) == RunsXNumTimePoints
+    TCSMask(:, :, iS) = repmat(1, PFMdim, RunsXNumTimePoints, 1);
+    if isempty(spectra)
+      spectra = SpectraSub;
+      spectra.cdata = SpectraSub.cdata * 0;
+    end
+    spectra.cdata = spectra.cdata + SpectraSub.cdata;
+  end
+  
+  % Accumulate spatial maps from all subjects with valid data
+  if isempty(PFMmaps)
+    PFMmaps = PFMMapsSub;
+    PFMmaps.cdata = PFMMapsSub.cdata * 0;
+    PFMvolMaps = PFMVolMapsSub;
+    PFMvolMaps.cdata = PFMVolMapsSub.cdata * 0;
+  end
+  PFMmaps.cdata = PFMmaps.cdata + PFMMapsSub.cdata;
+  PFMvolMaps.cdata = PFMvolMaps.cdata + PFMVolMapsSub.cdata;
+end  % for iS = 1:nS
+
+%% Create output directory if needed
+if ~exist(PFMFolder, 'dir'); mkdir(PFMFolder); end
+dimStr = num2str(PFMdim);
+
+%% Concatenate and reshape group time courses
+% Create single concatenated time series from all subjects
+TCSMaskConcat = TCSSub;
+TCSMaskConcat.cdata = squeeze(reshape(TCSMask, PFMdim, RunsXNumTimePoints * nS));
+TCSFullConcat = TCSSub;
+TCSFullConcat.cdata = squeeze(reshape(TCSAll, PFMdim, RunsXNumTimePoints * nS));
+ciftisavereset(TCSMaskConcat, [PFMFolder '/PFM_TCSMASK_' dimStr '.sdseries.nii'], wbcommand);
+ciftisavereset(TCSFullConcat, [PFMFolder '/PFM_TCS_' dimStr '.sdseries.nii'], wbcommand);
+
+%% Compute group average time courses
+% Calculate mean time course and mean absolute value time course
+TCSAVG = TCSSub;
+TCSAVG.cdata = sum(TCSAll .* TCSMask, 3) / nS;
+TCSABSAVG = TCSSub;
+TCSABSAVG.cdata = sum(abs(TCSAll .* TCSMask), 3) / nS;
+ciftisavereset(TCSAVG, [PFMFolder '/PFM_AVGTCS_' dimStr '.sdseries.nii'], wbcommand);
+ciftisavereset(TCSABSAVG, [PFMFolder '/PFM_ABSAVGTCS_' dimStr '.sdseries.nii'], wbcommand);
+
+%% Compute group-level statistics
+% Calculate variance explained by each PFM component
+PFMTSTDs = std(TCSFullConcat.cdata, [], 2);
+PFMPercentVariances = (((PFMTSTDs .^ 2) / sum(PFMTSTDs .^ 2)) * 100);
+dlmwrite([PFMFolder '/PFM_stats_' dimStr '.wb_annsub.csv'], [(1:PFMdim)' round(PFMPercentVariances, 2)], ',');
+
+%% Average group spectra
+% Normalize by number of subjects with valid data
+spectra.cdata = spectra.cdata / nS;
+ciftisavereset(spectra, [PFMFolder '/PFM_Spectra_' dimStr '.sdseries.nii'], wbcommand);
+
+%% Average group spatial maps
+% Compute mean PFM maps across all subjects
+PFMmaps.cdata = PFMmaps.cdata / nS;
+PFMvolMaps.cdata = PFMvolMaps.cdata / nS;
+
+%% Save group-level spatial maps
+% Output group-averaged surface and volume PFM maps
+ciftisavereset(PFMmaps, [PFMFolder '/PFM_Maps_' num2str(PFMdim) '.dscalar.nii'], wbcommand);
+ciftisavereset(PFMvolMaps, [PFMFolder '/PFM_VolMaps_' num2str(PFMdim) '.dscalar.nii'], wbcommand);
+end
\ No newline at end of file
diff --git a/PFM/scripts/GroupPFMs.sh b/PFM/scripts/GroupPFMs.sh
new file mode 100755
index 000000000..fe0429de4
--- /dev/null
+++ b/PFM/scripts/GroupPFMs.sh
@@ -0,0 +1,99 @@
+#!/bin/bash
+set -eu
+
+pipedirguessed=0
+if [[ "${HCPPIPEDIR:-}" == "" ]]
+then
+    pipedirguessed=1
+    export HCPPIPEDIR="$(dirname -- "$0")/../.."
+fi
+
+source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
+source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
+source "$HCPPIPEDIR/global/scripts/tempfiles.shlib"
+g_matlab_default_mode=1
+
+opts_SetScriptDescription "Aggregate individual subject PFM results and compute group-level time course masks, spectra, maps, and statistics"
+
+#arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
+opts_AddMandatory '--study-folder' 'StudyFolder' 'path' "folder that contains all subjects"
+opts_AddMandatory '--subject-list' 'SubjlistRaw' '100206@100307...' "list of subject IDs separated by @s"
+opts_AddMandatory '--pfm-dimension' 'PFMdim' 'integer' "PFM dimensionality (e.g., 76, 92, 65)"
+opts_AddMandatory '--output-string' 'OutputSTRING' 'string' "output string for files"
+opts_AddMandatory '--surf-reg-name' 'RegName' 'MSMAll' "the registration string corresponding to the input files"
+opts_AddMandatory '--low-res-mesh' 'LowResMesh' 'string' "mesh resolution"
+opts_AddMandatory '--runs-timepoints' 'RunsXNumTimePoints' 'integer' "total timepoints across runs (e.g., 4800 for rest, 3880 for task)"
+opts_AddMandatory '--pfm-folder' 'PFMFolder' 'path' "path to PFM results folder"
+opts_AddOptional '--matlab-run-mode' 'MatlabMode' '0, 1, or 2' "defaults to $g_matlab_default_mode
+0 = compiled MATLAB
+1 = interpreted MATLAB  
+2 = Octave" "$g_matlab_default_mode"
+
+opts_ParseArguments "$@"
+
+if ((pipedirguessed))
+then
+    log_Err_Abort "HCPPIPEDIR is not set, you must first source your edited copy of Examples/Scripts/SetUpHCPPipeline.sh"
+fi
+
+#display the parsed/default values
+opts_ShowValues
+
+RegString=""
+if [[ "$RegName" != "" ]]
+then
+    RegString="_$RegName"
+fi
+
+case "$MatlabMode" in
+    (0)
+        if [[ "${MATLAB_COMPILER_RUNTIME:-}" == "" ]]
+        then
+            log_Err_Abort "to use compiled matlab, you must set and export the variable MATLAB_COMPILER_RUNTIME"
+        fi
+        ;;
+    (1)
+        matlab_interpreter=(matlab -nodisplay -nosplash)
+        ;;
+    (2)
+        matlab_interpreter=(octave-cli -q --no-window-system)
+        ;;
+    (*)
+        log_Err_Abort "unrecognized matlab mode '$MatlabMode', use 0, 1, or 2"
+        ;;
+esac
+
+#shortcut in case the folder gets renamed
+this_script_dir=$(dirname "$0")
+
+#matlab function arguments converted to strings
+matlab_argarray=("$StudyFolder" "$SubjlistRaw" "$PFMdim" "$OutputSTRING" "$RegString" "$LowResMesh" "$RunsXNumTimePoints" "$PFMFolder")
+
+case "$MatlabMode" in
+    (0)
+        matlab_cmd=("$this_script_dir/Compiled_GroupPFMs/run_GroupPFMs.sh" "$MATLAB_COMPILER_RUNTIME" "${matlab_argarray[@]}")
+        log_Msg "running compiled matlab command: ${matlab_cmd[*]}"
+        "${matlab_cmd[@]}"
+        ;;
+    (1 | 2)
+        #reformat argument array so matlab sees them as strings
+        matlab_args=""
+        for thisarg in "${matlab_argarray[@]}"
+        do
+            if [[ "$matlab_args" != "" ]]
+            then
+                matlab_args+=", "
+            fi
+            matlab_args+="'$thisarg'"
+        done
+        matlabcode="
+            addpath('$HCPPIPEDIR/global/matlab');
+            addpath('$this_script_dir');
+            addpath('$HCPCIFTIRWDIR');
+            GroupPFMs($matlab_args);"
+
+        log_Msg "running matlab code: $matlabcode"
+        "${matlab_interpreter[@]}" <<<"$matlabcode"
+        echo
+        ;;
+esac
\ No newline at end of file
diff --git a/PFM/scripts/PostPROFUMO.m b/PFM/scripts/PostPROFUMO.m
new file mode 100755
index 000000000..346a34700
--- /dev/null
+++ b/PFM/scripts/PostPROFUMO.m
@@ -0,0 +1,149 @@
+function PostPROFUMO(StudyFolder, SubjListRaw, fMRIListRaw, ConcatName, fMRIProcSTRING, OutputfMRIName, OutputSTRING, RegString, LowResMesh, TR, PFMFolder,VarNormBool,VAweightBool)
+% PostPROFUMO(StudyFolder, SubjListRaw, fMRIListRaw, ConcatName, fMRIProcSTRING, OutputfMRIName, OutputSTRING, RegString, LowResMesh, TR, PFMFolder)
+% This function imports PROFUMO results and generates CIFTI-format time courses
+% and power spectra for each subject. The outputs are used for subsequent
+% group-level PFM analysis.
+%
+% Inputs:
+%   StudyFolder - Path to the study directory
+%   SubjListRaw - Subject list as @ separated string
+%   fMRIListRaw - fMRI run names as @ separated string
+%   ConcatName - Name of concatenated fMRI dataset (empty if single runs)
+%   fMRIProcSTRING - Processing string component (e.g., '_Atlas_hp200_clean')
+%   OutputfMRIName - Name of output fMRI dataset
+%   OutputSTRING - Output string for files
+%   RegString - Registration string
+%   LowResMesh - Mesh resolution (e.g., '10' for 10k)
+%   TR - Repetition time in seconds
+%   PFMFolder - Path to PROFUMO results folder
+%   VarNormBool - Boolean flag for variance normalization
+%   VAweightBool - Boolean flag for vertex area weighting
+
+%% Parse string inputs and initialize
+Subjlist = strsplit(SubjListRaw, '@');
+fMRINames = strsplit(fMRIListRaw, '@');
+TR = str2double(TR);
+VarNormBool = logical(str2double(VarNormBool));
+VAweightBool = logical(str2double(VAweightBool));
+wbcommand = 'wb_command';
+
+%% Main loop: Process each subject
+for s = 1:numel(Subjlist)
+    fprintf('Processing subject %d/%d: %s\n', s, numel(Subjlist), Subjlist{s});
+  
+    %% Identify available fMRI runs for this subject
+    % Determine which fMRI runs exist for this subject
+    % If ConcatName is specified, use concatenated version; otherwise check individual runs
+    subfMRINames = {};
+    if ~strcmp(ConcatName, '')
+        % Multi-run data: check if concatenated dataset exists
+        if exist([StudyFolder '/' Subjlist{s} '/MNINonLinear/Results/' ConcatName '/' ConcatName fMRIProcSTRING '.dtseries.nii'],'file')
+            c = 1;
+            for r = 1:numel(fMRINames)
+                if exist([StudyFolder '/' Subjlist{s} '/MNINonLinear/Results/' fMRINames{r} '/' fMRINames{r} fMRIProcSTRING '.dtseries.nii'],'file')
+                    subfMRINames{c} = fMRINames{r};
+                    c = c + 1;
+                end
+            end  % for r = 1:numel(fMRINames)            
+        end
+    else
+        % Single-run data: check which runs exist
+        c = 1;
+        for r = 1:numel(fMRINames)
+            if exist([StudyFolder '/' Subjlist{s} '/MNINonLinear/Results/' fMRINames{r} '/' fMRINames{r} fMRIProcSTRING '.dtseries.nii'],'file')
+                subfMRINames{c} = fMRINames{r};
+                c = c + 1;
+            end
+        end  % for r = 1:numel(fMRINames)
+    end
+  
+    %% Process subject if valid runs found
+    if numel(subfMRINames) ~= 0
+    
+        if VAweightBool
+          %  create temporary VA_norm cifti with volume grayordinates filled with ones areas for weighting 
+          ciftiTemplate = [StudyFolder '/' Subjlist{s} '/MNINonLinear/Results/' ConcatName '/' ConcatName RegString fMRIProcSTRING '_vn.dscalar.nii']; % use clean_VN as cifti template
+          VAnorm = [StudyFolder '/' Subjlist{s} '/T1w/fsaverage_LR' LowResMesh 'k/' Subjlist{s} '.midthickness' RegString '_va_norm.' LowResMesh 'k_fs_LR.dscalar.nii'];
+          tmp_VAgray_file = [tempname '.dscalar.nii'];
+          tmp_jnk_file = [tempname '.nii.gz'];
+          tmp_roi_file = [tempname '.nii.gz'];
+          system(sprintf('%s -cifti-separate "%s" COLUMN -volume-all "%s" -roi "%s" -crop', wbcommand, ciftiTemplate, tmp_jnk_file, tmp_roi_file));
+          system(sprintf('%s -cifti-create-dense-from-template "%s" "%s" -cifti "%s" -volume-all "%s" -from-cropped', wbcommand, ciftiTemplate, tmp_VAgray_file, VAnorm, tmp_roi_file));
+        end
+
+        %% Load and concatenate PFM time courses and amplitudes
+        % Load PROFUMO outputs and amplitude-modulate time courses
+        origTCS = [];  % Original unmodulated time courses
+        TCS = [];      % Amplitude-modulated time courses
+        for r = 1:numel(subfMRINames)
+            runTCS = load([PFMFolder '/Results.ppp/TimeCourses/sub-' Subjlist{s} '_run-' subfMRINames{r} '.csv']);
+            runAmp = load([PFMFolder '/Results.ppp/Amplitudes/sub-' Subjlist{s} '_run-' subfMRINames{r} '.csv']);
+
+            origTCS = [origTCS ; runTCS];
+            TCS = [TCS ; runTCS .* repmat(runAmp', size(runTCS, 1), 1)];
+            end  % for r = 1:numel(subfMRINames)
+        
+        %% Create original time course and spectral CIFTI files
+        % Generate CIFTI structure for unmodulated time courses
+        PFMTCSorig = cifti_struct_create_sdseries(origTCS','step',TR);
+        
+        % Store power spectra 
+        ts.Nnodes = size(origTCS, 2);
+        ts.Nsubjects = 1;
+        ts.ts = origTCS;
+        ts.NtimepointsPerSubject = size(origTCS, 1);
+        PFMSpectraorig = cifti_struct_create_sdseries(nets_spectra_sp(ts)','step',1/TR);
+        
+        %% Create  time course and spectral CIFTI files
+        % Generate CIFTI structure for  time courses
+        PFMTCS = cifti_struct_create_sdseries(TCS','step',TR);
+        
+        % Store power spectra 
+        ts.Nnodes = size(TCS, 2);
+        ts.Nsubjects = 1;
+        ts.ts = TCS;
+        ts.NtimepointsPerSubject = size(TCS, 1);
+        PFMSpectra = cifti_struct_create_sdseries(nets_spectra_sp(ts)','step',1/TR);
+
+        %% Save non-map results
+        % Save original and amplitude-modulated time courses and spectra
+        ciftisave(PFMTCSorig, [StudyFolder '/' Subjlist{s} '/MNINonLinear/fsaverage_LR' LowResMesh 'k/' Subjlist{s} '.' OutputSTRING RegString '_ts_orig.' LowResMesh 'k_fs_LR.sdseries.nii'], wbcommand);
+        ciftisave(PFMSpectraorig, [StudyFolder '/' Subjlist{s} '/MNINonLinear/fsaverage_LR' LowResMesh 'k/' Subjlist{s} '.' OutputSTRING RegString '_spectra_orig.' LowResMesh 'k_fs_LR.sdseries.nii'], wbcommand);
+
+        ciftisave(PFMTCS, [StudyFolder '/' Subjlist{s} '/MNINonLinear/fsaverage_LR' LowResMesh 'k/' Subjlist{s} '.' OutputSTRING RegString '_ts.' LowResMesh 'k_fs_LR.sdseries.nii'], wbcommand);
+        ciftisave(PFMSpectra, [StudyFolder '/' Subjlist{s} '/MNINonLinear/fsaverage_LR' LowResMesh 'k/' Subjlist{s} '.' OutputSTRING RegString '_spectra.' LowResMesh 'k_fs_LR.sdseries.nii'], wbcommand);
+
+        %% Handle maps
+        % restore variance
+        if VarNormBool
+            fprintf('Restoring variance\n');
+            clean_VN_Name = [StudyFolder '/' Subjlist{s} '/MNINonLinear/Results/' ConcatName '/' ConcatName RegString fMRIProcSTRING '_vn.dscalar.nii'];
+            clean_VN = ciftiopen(clean_VN_Name, wbcommand).cdata;
+            mapFile = [PFMFolder '/Results.ppp/Maps/sub-' Subjlist{s} '.dscalar.nii'];
+            maps = ciftiopen(mapFile, wbcommand);
+            maps.cdata = maps.cdata .* clean_VN;
+            ciftisave(maps, mapFile, wbcommand);
+        end
+
+        % divide out vertex area weights
+        if VAweightBool
+            fprintf('Dividing out vertex area weights\n');
+            VAgray = ciftiopen([StudyFolder '/' Subjlist{s} '/T1w/fsaverage_LR' LowResMesh 'k/' Subjlist{s} '.midthickness' RegString '_va_norm.grayordinates.' LowResMesh 'k_fs_LR.dscalar.nii'], wbcommand).cdata;
+            mapFile = [PFMFolder '/Results.ppp/Maps/sub-' Subjlist{s} '.dscalar.nii'];
+            maps = ciftiopen(mapFile, wbcommand);
+            maps.cdata = maps.cdata ./ VAgray;
+            ciftisave(maps, mapFile, wbcommand);
+        end
+        
+        % Copy PFM maps from PFM folder to subject's MNINonLinear/fsaverage_LR<LowResMesh> space directory
+        copyfile([PFMFolder '/Results.ppp/Maps/sub-' Subjlist{s} '.dscalar.nii'], [StudyFolder '/' Subjlist{s} '/MNINonLinear/fsaverage_LR' LowResMesh 'k/' Subjlist{s} '.' OutputSTRING RegString '_origmaps.' LowResMesh 'k_fs_LR.dscalar.nii']);
+
+        % clean up temporary files
+        if VAweightBool
+          delete(tmp_VAgray_file);
+          delete(tmp_roi_file);
+          delete(tmp_jnk_file);
+        end
+    end  % if numel(subfMRINames) ~= 0
+end  % for s = 1:numel(Subjlist)
+end
diff --git a/PFM/scripts/PostPROFUMO.sh b/PFM/scripts/PostPROFUMO.sh
new file mode 100755
index 000000000..5c29bf014
--- /dev/null
+++ b/PFM/scripts/PostPROFUMO.sh
@@ -0,0 +1,112 @@
+#!/bin/bash
+set -eu
+
+pipedirguessed=0
+if [[ "${HCPPIPEDIR:-}" == "" ]]
+then
+    pipedirguessed=1
+    export HCPPIPEDIR="$(dirname -- "$0")/../.."
+fi
+
+source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
+source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
+source "$HCPPIPEDIR/global/scripts/tempfiles.shlib"
+g_matlab_default_mode=1
+
+#description of this script to use in usage
+opts_SetScriptDescription "Import PROFUMO outputs and create time courses, spectra, and maps"
+
+#arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
+opts_AddMandatory '--study-folder' 'StudyFolder' 'path' "folder containing all subjects"
+opts_AddMandatory '--subject-list' 'SubjListRaw' '100206@100307...' 'list of subject IDs separated by @s'
+opts_AddMandatory '--fmri-names' 'fMRIListRaw' 'rfMRI_REST1_LR@rfMRI_REST1_RL...' 'list of fmri run names separated by @s'
+opts_AddMandatory '--proc-string' 'fMRIProcSTRING' 'string' "file name component representing the preprocessing"
+opts_AddMandatory '--output-fmri-name' 'OutputfMRIName' 'rfMRI_REST' "name to use for PFM pipeline outputs"
+opts_AddMandatory '--output-string' 'OutputSTRING' 'string' "output string for files"
+opts_AddMandatory '--surf-reg-name' 'RegName' 'MSMAll' "the registration string"
+opts_AddMandatory '--low-res-mesh' 'LowResMesh' 'string' "mesh resolution"
+opts_AddMandatory '--pfm-folder' 'PFMFolder' 'path' "path to PFM results folder"
+opts_AddMandatory '--concat-name' 'ConcatName' 'string' "concatenated fMRI name if using multi-run data"
+opts_AddMandatory '--profumo-tr' 'TR' "repetition time for PROFUMO analysis" '0.72'
+opts_AddOptional '--variance-normalize' 'VarNorm' 'YES or NO' "Data were variance normalized before PROFUMO, so restore varaince (default YES)" 'YES'
+opts_AddOptional '--weight-vertex-areas' 'VAweight' 'YES or NO' "Data were weighted by vertex areas before PROFUMO, so restore unweighted state (default YES)" 'YES'
+
+opts_AddOptional '--matlab-run-mode' 'MatlabMode' '0, 1, or 2' "defaults to $g_matlab_default_mode
+0 = compiled MATLAB
+1 = interpreted MATLAB  
+2 = Octave" "$g_matlab_default_mode"
+
+opts_ParseArguments "$@"
+VarNormBool=$(opts_StringToBool "$VarNorm")
+VAweightBool=$(opts_StringToBool "$VAweight")
+
+
+if ((pipedirguessed))
+then
+    log_Err_Abort "HCPPIPEDIR is not set, you must first source your edited copy of Examples/Scripts/SetUpHCPPipeline.sh"
+fi
+
+#display the parsed/default values
+opts_ShowValues
+
+RegString=""
+if [[ "$RegName" != "" ]]
+then
+    RegString="_$RegName"
+fi
+
+case "$MatlabMode" in
+    (0)
+        if [[ "${MATLAB_COMPILER_RUNTIME:-}" == "" ]]
+        then
+            log_Err_Abort "to use compiled matlab, you must set and export the variable MATLAB_COMPILER_RUNTIME"
+        fi
+        ;;
+    (1)
+        matlab_interpreter=(matlab -nodisplay -nosplash)
+        ;;
+    (2)
+        matlab_interpreter=(octave-cli -q --no-window-system)
+        ;;
+    (*)
+        log_Err_Abort "unrecognized matlab mode '$MatlabMode', use 0, 1, or 2"
+        ;;
+esac
+
+IFS='@' read -a SubjList <<<"$SubjListRaw"
+IFS='@' read -a fMRIList <<<"$fMRIListRaw"
+
+#shortcut in case the folder gets renamed
+this_script_dir=$(dirname "$0")
+
+#matlab function arguments converted to strings
+matlab_argarray=("$StudyFolder" "$SubjListRaw" "$fMRIListRaw" "$ConcatName" "$fMRIProcSTRING" "$OutputfMRIName" "$OutputSTRING" "$RegString" "$LowResMesh" "$TR" "$PFMFolder" "$VarNormBool" "$VAweightBool")
+
+case "$MatlabMode" in
+    (0)
+        matlab_cmd=("$this_script_dir/Compiled_PostPROFUMO/run_PostPROFUMO.sh" "$MATLAB_COMPILER_RUNTIME" "${matlab_argarray[@]}")
+        log_Msg "running compiled matlab command: ${matlab_cmd[*]}"
+        "${matlab_cmd[@]}"
+        ;;
+    (1 | 2)
+        #reformat argument array so matlab sees them as strings
+        matlab_args=""
+        for thisarg in "${matlab_argarray[@]}"
+        do
+            if [[ "$matlab_args" != "" ]]
+            then
+                matlab_args+=", "
+            fi
+            matlab_args+="'$thisarg'"
+        done
+        matlabcode="
+            addpath('$HCPPIPEDIR/global/matlab');
+            addpath('$this_script_dir');
+            addpath('$HCPCIFTIRWDIR');
+            PostPROFUMO($matlab_args);"
+
+        log_Msg "running matlab code: $matlabcode"
+        "${matlab_interpreter[@]}" <<<"$matlabcode"
+        echo
+        ;;
+esac
\ No newline at end of file
diff --git a/PostFreeSurfer/PostFreeSurferPipeline.sh b/PostFreeSurfer/PostFreeSurferPipeline.sh
index f2e0944a8..03be00da1 100755
--- a/PostFreeSurfer/PostFreeSurferPipeline.sh
+++ b/PostFreeSurfer/PostFreeSurferPipeline.sh
@@ -50,27 +50,13 @@ source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/processingmodecheck.shlib" "$@" # Check processing mode requirements
 
+#description of this script to use in usage
+opts_SetScriptDescription "takes FreeSurfer output folder and converts files into HCP format/organization, etc."
+
 log_Msg "Platform Information Follows: "
 uname -a
 "$HCPPIPEDIR"/show_version
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: takes FreeSurfer output folder and converts files into HCP format/organization, etc.
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
-
 defaultSigma=$(echo "sqrt(200)" | bc -l)
 
 opts_AddMandatory '--study-folder' 'StudyFolder' 'path' "folder containing all subjects" "--path"
diff --git a/PostFreeSurfer/PostFreeSurferPipeline_1res.sh b/PostFreeSurfer/PostFreeSurferPipeline_1res.sh
index 365d4b6b3..3ed080274 100755
--- a/PostFreeSurfer/PostFreeSurferPipeline_1res.sh
+++ b/PostFreeSurfer/PostFreeSurferPipeline_1res.sh
@@ -26,27 +26,13 @@ source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/processingmodecheck.shlib" "$@" # Check processing mode requirements
 
+#description of this script to use in usage
+opts_SetScriptDescription "takes FreeSurfer output folder and converts files into HCP format/organization, etc."
+
 log_Msg "Platform Information Follows: "
 uname -a
 "$HCPPIPEDIR"/show_version
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: takes FreeSurfer output folder and converts files into HCP format/organization, etc.
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
-
 defaultSigma=$(echo "sqrt(200)" | bc -l)
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
diff --git a/PostFreeSurfer/scripts/GenerateStructuralScenes.sh b/PostFreeSurfer/scripts/GenerateStructuralScenes.sh
index e6bbdd26b..2cd2cb022 100755
--- a/PostFreeSurfer/scripts/GenerateStructuralScenes.sh
+++ b/PostFreeSurfer/scripts/GenerateStructuralScenes.sh
@@ -13,22 +13,8 @@ source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/tempfiles.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/relativePath.shlib" "$@"
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: makes QC scenes and captures for HCP FreeSurfer pipelines
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
+#description of this script to use in usage
+opts_SetScriptDescription "makes QC scenes and captures for HCP FreeSurfer pipelines"
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
 #help info for option gets printed like "--foo=<$3> - $4"
diff --git a/TaskfMRIAnalysis/TaskfMRIAnalysis.sh b/TaskfMRIAnalysis/TaskfMRIAnalysis.sh
index 9f187fb10..75a6ff9a2 100755
--- a/TaskfMRIAnalysis/TaskfMRIAnalysis.sh
+++ b/TaskfMRIAnalysis/TaskfMRIAnalysis.sh
@@ -57,29 +57,16 @@ source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/fsl_version.shlib"	# Function for getting FSL version
 
 
-# --------------------------------------------------------------------------------
-#  Usage Description Function
-# --------------------------------------------------------------------------------
+# -------------------------------------------------------
+#  Usage Description
+# -------------------------------------------------------
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: Run TaskfMRIAnalysis pipeline for a subject. Pipeline will run Level1 (scan-level) analyses, and Level2 (single subject-level) analysis as specified.
-
-Usage: $log_ToolName arguments...
-[ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
+#description of this script to use in usage
+opts_SetScriptDescription "Run TaskfMRIAnalysis pipeline for a subject. Pipeline will run Level1 (scan-level) analyses, and Level2 (single subject-level) analysis as specified."
 
-# ------------------------------------------------------------------------------
+# -------------------------------------------
 #  Parse Command Line Options
-# ------------------------------------------------------------------------------
+# -------------------------------------------
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
 #help info for option gets printed like "--foo=<$3> - $4"
diff --git a/TaskfMRIAnalysis/scripts/makeSubjectTaskSummary.sh b/TaskfMRIAnalysis/scripts/makeSubjectTaskSummary.sh
index ed6866b87..d35633738 100755
--- a/TaskfMRIAnalysis/scripts/makeSubjectTaskSummary.sh
+++ b/TaskfMRIAnalysis/scripts/makeSubjectTaskSummary.sh
@@ -55,29 +55,16 @@ source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/fsl_version.shlib"	# Function for getting FSL version
 
 
-# --------------------------------------------------------------------------------
-#  Usage Description Function
-# --------------------------------------------------------------------------------
-
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: Run TaskfMRIAnalysis pipeline for a subject. Pipeline will run Level1 (scan-level) analyses, and Level2 (single subject-level) analysis as specified.
-
-Usage: $log_ToolName arguments...
-[ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
+# -------------------------------------------
+#  Usage Description
+# -------------------------------------------
 
-# ------------------------------------------------------------------------------
+#description of this script to use in usage
+opts_SetScriptDescription "Run TaskfMRIAnalysis pipeline for a subject. Pipeline will run Level1 (scan-level) analyses, and Level2 (single subject-level) analysis as specified."
+
+# -------------------------------------------
 #  Parse Command Line Options
-# ------------------------------------------------------------------------------
+# -------------------------------------------
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
 #help info for option gets printed like "--foo=<$3> - $4"
diff --git a/fMRISurface/scripts/GenerateFMRIScenes.sh b/fMRISurface/scripts/GenerateFMRIScenes.sh
index 31c98860b..d63654163 100755
--- a/fMRISurface/scripts/GenerateFMRIScenes.sh
+++ b/fMRISurface/scripts/GenerateFMRIScenes.sh
@@ -12,22 +12,8 @@ source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/relativePath.shlib" "$@"
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: makes QC scenes and captures for HCP fMRIVolume pipeline
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
+#description of this script to use in usage
+opts_SetScriptDescription "makes QC scenes and captures for HCP fMRIVolume pipeline"
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
 #help info for option gets printed like "--foo=<$3> - $4"
diff --git a/global/scripts/ExtractFromMRFIXConcat.sh b/global/scripts/ExtractFromMRFIXConcat.sh
index f0a33a8a5..192e8d878 100755
--- a/global/scripts/ExtractFromMRFIXConcat.sh
+++ b/global/scripts/ExtractFromMRFIXConcat.sh
@@ -11,24 +11,8 @@ fi
 source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: extract a specified set of runs from an MR FIX
-    concatenated file and reconcatenate them.  Typically this is used to extract
-    the resting state runs from a combined task and resting state MR FIX run.
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
+#description of this script to use in usage
+opts_SetScriptDescription "extract a specified set of runs from an MR FIX concatenated file and reconcatenate them.  Typically this is used to extract the resting state runs from a combined task and resting state MR FIX run."
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
 #help info for option gets printed like "--foo=<$3> - $4"
diff --git a/global/scripts/RSNregression.sh b/global/scripts/RSNregression.sh
index 5e901a941..09f23a98f 100755
--- a/global/scripts/RSNregression.sh
+++ b/global/scripts/RSNregression.sh
@@ -13,20 +13,8 @@ source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/tempfiles.shlib"
 g_matlab_default_mode=1
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: regresses group ICA spatial maps into individual data in order to obtain individual spatial maps of where the subject's similar function is
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-}
+#description of this script to use in usage
+opts_SetScriptDescription "regresses group ICA spatial maps into individual data in order to obtain individual spatial maps of where the subject's similar function is"
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value other than empty string if AddOptional], [compatibility flag, ...]
 opts_AddMandatory '--study-folder' 'StudyFolder' 'path' "folder containing all subjects"
diff --git a/tICA/scripts/ComputeGroupTICA.sh b/tICA/scripts/ComputeGroupTICA.sh
index 89b0c4ae4..e995bae7a 100755
--- a/tICA/scripts/ComputeGroupTICA.sh
+++ b/tICA/scripts/ComputeGroupTICA.sh
@@ -13,22 +13,8 @@ source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/tempfiles.shlib"
 g_matlab_default_mode=1
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: does stuff
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
+#description of this script to use in usage
+opts_SetScriptDescription "does stuff"
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
 #help info for option gets printed like "--foo=<$3> - $4"
diff --git a/tICA/scripts/ComputeTICAFeatures.sh b/tICA/scripts/ComputeTICAFeatures.sh
index 486ae6472..a5890bd1b 100755
--- a/tICA/scripts/ComputeTICAFeatures.sh
+++ b/tICA/scripts/ComputeTICAFeatures.sh
@@ -14,22 +14,8 @@ source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/tempfiles.shlib"
 g_matlab_default_mode=1
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: does stuff
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
+#description of this script to use in usage
+opts_SetScriptDescription "does stuff"
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
 #help info for option gets printed like "--foo=<$3> - $4"
diff --git a/tICA/scripts/ConcatGroupSICA.sh b/tICA/scripts/ConcatGroupSICA.sh
index d39e4063a..e39ad6de5 100755
--- a/tICA/scripts/ConcatGroupSICA.sh
+++ b/tICA/scripts/ConcatGroupSICA.sh
@@ -13,22 +13,8 @@ source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/tempfiles.shlib"
 g_matlab_default_mode=1
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: does stuff
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
+#description of this script to use in usage
+opts_SetScriptDescription "does stuff"
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
 #help info for option gets printed like "--foo=<$3> - $4"
diff --git a/tICA/scripts/GroupSICA.sh b/tICA/scripts/GroupSICA.sh
index 40e08789a..8cac4e9f2 100755
--- a/tICA/scripts/GroupSICA.sh
+++ b/tICA/scripts/GroupSICA.sh
@@ -12,22 +12,8 @@ source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 g_matlab_default_mode=1
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: does stuff
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
+#description of this script to use in usage
+opts_SetScriptDescription "does stuff"
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
 #help info for option gets printed like "--foo=<$3> - $4"
diff --git a/tICA/scripts/MIGP.sh b/tICA/scripts/MIGP.sh
index c4affb1e0..51d2a5503 100755
--- a/tICA/scripts/MIGP.sh
+++ b/tICA/scripts/MIGP.sh
@@ -13,22 +13,8 @@ source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/tempfiles.shlib"
 g_matlab_default_mode=1
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: does stuff
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-    
-    #do not use exit, the parsing code takes care of it
-}
+#description of this script to use in usage
+opts_SetScriptDescription "does stuff"
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value if AddOptional], [compatibility flag, ...]
 #help info for option gets printed like "--foo=<$3> - $4"
diff --git a/tICA/scripts/tICACleanData.sh b/tICA/scripts/tICACleanData.sh
index 16ae27452..e1702688d 100755
--- a/tICA/scripts/tICACleanData.sh
+++ b/tICA/scripts/tICACleanData.sh
@@ -13,20 +13,8 @@ source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@"
 source "$HCPPIPEDIR/global/scripts/tempfiles.shlib" "$@"
 g_matlab_default_mode=1
 
-#this function gets called by opts_ParseArguments when --help is specified
-function usage()
-{
-    #header text
-    echo "
-$log_ToolName: regresses noise group temporal ICA components out of CIFTI and optionaly volume timeseries data and optionally correct the bias legacy field
-
-Usage: $log_ToolName PARAMETER...
-
-PARAMETERs are [ ] = optional; < > = user supplied value
-"
-    #automatic argument descriptions
-    opts_ShowArguments
-}
+#description of this script to use in usage
+opts_SetScriptDescription "regresses noise group temporal ICA components out of CIFTI and optionally volume timeseries data and optionally correct the bias legacy field"
 
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value other than empty string if AddOptional], [compatibility flag, ...]
 opts_AddMandatory '--study-folder' 'StudyFolder' 'path' "folder containing all subjects"