Add hippocampal fMRISurface processing

fMRISurface/GenericHippocampusfMRISurfaceProcessingPipeline.sh

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+#!/bin/bash
+
+# Requirements for this script
+# installed versions of: FSL, Connectome Workbench (wb_command)
+# environment: HCPPIPEDIR, FSLDIR, CARET7DIR
+
+########################################## PIPELINE OVERVIEW ##########################################
+
+# TODO
+
+########################################## OUTPUT DIRECTORIES ##########################################
+
+# TODO
+
+################################################ SUPPORT FUNCTIONS ##################################################
+
+set -eu
+pipedirguessed=0
+if [[ "${HCPPIPEDIR:-}" == "" ]]
+then
+    pipedirguessed=1
+    # Fix this if the script is more than one level below HCPPIPEDIR
+    export HCPPIPEDIR="$(dirname -- "$0")/.."
+fi
+
+#comment the line back in when done
+source "${HCPPIPEDIR}/global/scripts/debug.shlib" "$@"          # Debugging functions; also sources log.shlib
+source "${HCPPIPEDIR}/global/scripts/newopts.shlib" "$@"
+source "${HCPPIPEDIR}/global/scripts/processingmodecheck.shlib" # Check processing mode requirements
+
+opts_SetScriptDescription "Run hippocampal fMRISurface processing"
+
+opts_AddMandatory '--studyfolder' 'Path' 'path' "folder containing all subjects" "--path"
+
+opts_AddMandatory '--subject' 'Subject' 'subject ID' ""
+
+opts_AddMandatory '--fmriname' 'NameOffMRI' 'string' 'fMRI run name, for example rfMRI_REST1_LR'
+
+opts_AddOptional '--procstring' 'ProcString' 'string' 'processing suffix appended to the 4D fMRI filename; include the leading underscore' ""
+
+opts_AddMandatory '--smoothingFWHM' 'SmoothingFWHM' 'number' 'smoothing FWHM (mm)'
+
+opts_AddOptional '--fmri-qc' 'QCMode' 'YES OR NO OR ONLY' "Controls whether to generate a QC scene and snapshots (default=YES). ONLY executes just the QC script." "YES"
+
+opts_AddOptional '--output-directory' 'OutputDirectory' 'path' 'Directory where pipeline outputs will be written' ""
+
+opts_AddOptional '--goodvoxel' 'doGoodVoxels' 'YES OR NO' "Controls whether to do goodVoxel procedure (default = YES)" "YES"
+
+opts_AddOptional '--factor' 'factor' 'number' "Scaling factor for eliminating high COV voxels"
+
+opts_ParseArguments "$@"
+
+if ((pipedirguessed))
+then
+    log_Err_Abort "HCPPIPEDIR is not set; first source your edited copy of Examples/Scripts/SetUpHCPPipeline.sh"
+fi
+
+opts_ShowValues
+
+"${HCPPIPEDIR}/show_version"
+
+# ------------------------------------------------------------------------------
+# Verify required environment variables are set
+# ------------------------------------------------------------------------------
+
+log_Check_Env_Var HCPPIPEDIR
+log_Check_Env_Var FSLDIR
+log_Check_Env_Var CARET7DIR
+
+HCPPIPEDIR_fMRISurf="${HCPPIPEDIR}/fMRISurface/scripts"
+
+# ------------------------------------------------------------------------------
+# Parse command-line options
+# ------------------------------------------------------------------------------
+
+log_Msg "Platform Information Follows:"
+uname -a
+
+QCMode="$(echo "${QCMode}" | tr '[:upper:]' '[:lower:]')"
+
+doProcessing=1
+doQC=1
+
+case "${QCMode}" in
+    yes)
+        ;;
+    no)
+        doQC=0
+        ;;
+    only)
+        doProcessing=0
+        log_Warn "Only generating fMRI QC scene and snapshots from existing data"
+        ;;
+    *)
+        log_Err_Abort "Unrecognized value '${QCMode}' for --fmri-qc; use YES, NO, or ONLY"
+        ;;
+esac
+
+
+# ------------------------------------------------------------------------------
+# Set up paths
+# ------------------------------------------------------------------------------
+
+PipelineScripts="${HCPPIPEDIR_fMRISurf}"
+
+MainSubjectFolder="${Path}/${Subject}"
+AtlasSpaceFolder="${MainSubjectFolder}/MNINonLinear"
+InputResultsFolder="${AtlasSpaceFolder}/Results/${NameOffMRI}"
+ResultsFolderName="Results"
+
+if [ -n "${OutputDirectory}" ]; then
+    ResultsFolder="${OutputDirectory}/${Subject}/${NameOffMRI}"
+else
+    ResultsFolder="${AtlasSpaceFolder}/${ResultsFolderName}/${NameOffMRI}"
+fi
+
+WorkingDirectory="${ResultsFolder}/tmp"
+
+mkdir -p "${WorkingDirectory}"
+
+VolumefMRI="${InputResultsFolder}/${NameOffMRI}${ProcString}"
+
+SBRef="${InputResultsFolder}/${NameOffMRI}_SBRef.nii.gz"
+
+HippUnfoldFolder="${AtlasSpaceFolder}/HippUnfold"
+
+if [ ! -f "${VolumefMRI}.nii.gz" ]; then
+    log_Err_Abort "Cannot find selected fMRI file: ${VolumefMRI}.nii.gz"
+fi
+
+if [ ! -f "${SBRef}" ]; then
+    log_Err_Abort "Cannot find selected SBRef file: ${SBRef}"
+fi
+
+log_Msg "Selected fMRI file: ${VolumefMRI}.nii.gz"
+log_Msg "Selected SBRef file: ${SBRef}"
+
+# ------------------------------------------------------------------------------
+# Generate fMRI time series within ROIs
+# ------------------------------------------------------------------------------
+
+if ((doProcessing)); then
+
+    # Make fMRI ribbon
+    log_Msg "Make fMRI Ribbon"
+    log_Msg "mkdir -p ${WorkingDirectory}"
+
+    log_Msg "Hippocampal Volume To Surface Mapping"
+    "${PipelineScripts}/HippocampalVolumeToSurfaceMapping.sh" \
+            "${WorkingDirectory}" \
+            "${Subject}" \
+            "${HippUnfoldFolder}" \
+            "${VolumefMRI}" \
+            "${SBRef}" \
+            "${doGoodVoxels}" \
+            "${factor}"
+
+#Surface Smoothing
+ # ------------------------------------------------------------------------------
+# Hippocampal Surface Smoothing
+# ------------------------------------------------------------------------------
+
+    log_Msg "Hippocampal Surface Smoothing"
+
+    Sigma=`echo "$SmoothingFWHM / (2 * sqrt(2 * l(2)))" | bc -l`
+
+    Meshes=(native 512 2k 8k 18k)
+    Structures=(hipp dentate)
+
+    for Mesh in "${Meshes[@]}"; do
+        for Structure in "${Structures[@]}"; do
+            for Hemisphere in L R; do
+                "${CARET7DIR}/wb_command" -metric-smoothing \
+                    "${HippUnfoldFolder}/${Mesh}/${Subject}.${Hemisphere}.${Structure}_midthickness.${Mesh}.surf.gii" \
+                    "${WorkingDirectory}/${Subject}.${Hemisphere}.${Structure}_fMRI.${Mesh}.func.gii" \
+                    "${Sigma}" \
+                    "${WorkingDirectory}/${Subject}.${Hemisphere}.${Structure}_fMRI_s${SmoothingFWHM}.${Mesh}.func.gii" \
+                    -roi "${WorkingDirectory}/${Subject}.${Hemisphere}.${Structure}_ones.${Mesh}.func.gii"
+            done
+        done
+    done
+# ------------------------------------------------------------------------------
+# Combining ROIs into a single CIFTI file
+# ------------------------------------------------------------------------------
+
+
+    for Mesh in ${Meshes[@]}; do
+        "${CARET7DIR}/wb_command" -cifti-create-dense-timeseries \
+            "${ResultsFolder}/${NameOffMRI}_AtlasHipp_${ProcString}.${Mesh}.dtseries.nii" \
+            -metric HIPPOCAMPUS_LEFT "${WorkingDirectory}/${Subject}.L.hipp_fMRI_s${SmoothingFWHM}.${Mesh}.func.gii" \
+                -roi "${WorkingDirectory}/${Subject}.L.hipp_ones.${Mesh}.func.gii" \
+            -metric HIPPOCAMPUS_RIGHT "${WorkingDirectory}/${Subject}.R.hipp_fMRI_s${SmoothingFWHM}.${Mesh}.func.gii" \
+                -roi "${WorkingDirectory}/${Subject}.R.hipp_ones.${Mesh}.func.gii" \
+            -metric HIPPOCAMPUS_DENTATE_LEFT "${WorkingDirectory}/${Subject}.L.dentate_fMRI_s${SmoothingFWHM}.${Mesh}.func.gii" \
+                -roi "${WorkingDirectory}/${Subject}.L.dentate_ones.${Mesh}.func.gii" \
+            -metric HIPPOCAMPUS_DENTATE_RIGHT "${WorkingDirectory}/${Subject}.R.dentate_fMRI_s${SmoothingFWHM}.${Mesh}.func.gii" \
+                -roi "${WorkingDirectory}/${Subject}.R.dentate_ones.${Mesh}.func.gii"
+
+            log_Msg "Generated fMRI time series Cifti file: "${ResultsFolder}/${Subject}.${NameOffMRI}"_AtlasHipp_${ProcString}.${Mesh}.dtseries.nii"
+
+# --------------------------------------------------------------------------
+# Combine VN maps from all four hippocampal structures
+# --------------------------------------------------------------------------
+
+    "${CARET7DIR}/wb_command" -cifti-create-dense-scalar \
+        "${ResultsFolder}/${NameOffMRI}_AtlasHipp_${ProcString}_vn.${Mesh}.dscalar.nii" \
+        -metric HIPPOCAMPUS_LEFT \
+            "${WorkingDirectory}/${Subject}.L.hipp_fMRI_vn.${Mesh}.func.gii" \
+            -roi "${WorkingDirectory}/${Subject}.L.hipp_ones.${Mesh}.func.gii" \
+        -metric HIPPOCAMPUS_RIGHT \
+            "${WorkingDirectory}/${Subject}.R.hipp_fMRI_vn.${Mesh}.func.gii" \
+            -roi "${WorkingDirectory}/${Subject}.R.hipp_ones.${Mesh}.func.gii" \
+        -metric HIPPOCAMPUS_DENTATE_LEFT \
+            "${WorkingDirectory}/${Subject}.L.dentate_fMRI_vn.${Mesh}.func.gii" \
+            -roi "${WorkingDirectory}/${Subject}.L.dentate_ones.${Mesh}.func.gii" \
+        -metric HIPPOCAMPUS_DENTATE_RIGHT \
+            "${WorkingDirectory}/${Subject}.R.dentate_fMRI_vn.${Mesh}.func.gii" \
+            -roi "${WorkingDirectory}/${Subject}.R.dentate_ones.${Mesh}.func.gii"
+
+    log_Msg "Generated VN CIFTI file: ${ResultsFolder}/${NameOffMRI}_AtlasHipp_${ProcString}_vn.${Mesh}.dscalar.nii"
+
+    done
+fi
+
+#Uncomment if want to remove the subfoler with intermediate files
+#rm -rf "${WorkingDirectory}"
+
+# if ((doQC)); then
+#     log_Msg "Generating fMRI QC scene and snapshots"
+#     "${PipelineScripts}/GenerateFMRIScenes.sh" \
+#         --study-folder="${Path}" \
+#         --subject="${Subject}" \
+#         --fmriname="${NameOffMRI}${ProcString}" \
+#         --output-folder="${ResultsFolder}/fMRIQC"
+# fi
+
+log_Msg "Completed!"