diff --git a/PostFreeSurfer/PostFreeSurferPipeline.sh b/PostFreeSurfer/PostFreeSurferPipeline.sh
index 6d5d54c83..4dacde0b7 100755
--- a/PostFreeSurfer/PostFreeSurferPipeline.sh
+++ b/PostFreeSurfer/PostFreeSurferPipeline.sh
@@ -12,17 +12,17 @@ set -e
 script_name=$(basename "${0}")
 
 if [ -z "${HCPPIPEDIR}" ]; then
-	echo "${script_name}: ABORTING: HCPPIPEDIR environment variable must be set"
-	exit 1
+  echo "${script_name}: ABORTING: HCPPIPEDIR environment variable must be set"
+  exit 1
 else
-	echo "${script_name}: HCPPIPEDIR: ${HCPPIPEDIR}"
+  echo "${script_name}: HCPPIPEDIR: ${HCPPIPEDIR}"
 fi
 
 if [ -z "${HCPPIPEDIR_PostFS}" ]; then
-	echo "${script_name}: ABORTING: HCPPIPEDIR_PostFS environment variable must be set"
-	exit 1
+  echo "${script_name}: ABORTING: HCPPIPEDIR_PostFS environment variable must be set"
+  exit 1
 else
-	echo "${script_name}: HCPPIPEDIR_PostFS: ${HCPPIPEDIR_PostFS}"
+  echo "${script_name}: HCPPIPEDIR_PostFS: ${HCPPIPEDIR_PostFS}"
 fi
 
 ########################################## PIPELINE OVERVIEW ##########################################
@@ -37,8 +37,9 @@ fi
 #  Load Function Libraries
 # --------------------------------------------------------------------------------
 
-source $HCPPIPEDIR/global/scripts/log.shlib  # Logging related functions
-source $HCPPIPEDIR/global/scripts/opts.shlib # Command line option functions
+source ${HCPPIPEDIR}/global/scripts/log.shlib   # Logging related functions
+source ${HCPPIPEDIR}/global/scripts/opts.shlib  # Command line option functions
+source ${HCPPIPEDIR}/global/scripts/processingmodecheck.shlib  # Checking processing mode compliance
 
 ########################################## SUPPORT FUNCTIONS ##########################################
 
@@ -80,16 +81,39 @@ ReferenceMyelinMaps=`opts_GetOpt1 "--refmyelinmaps" $@`
 CorrectionSigma=`opts_GetOpt1 "--mcsigma" $@`
 RegName=`opts_GetOpt1 "--regname" $@`
 InflateExtraScale=`opts_GetOpt1 "--inflatescale" $@`
+ProcessingMode=`opts_GetOpt1 "--processing-mode" $@`
 
 log_Msg "RegName: ${RegName}"
 
 # default parameters
 CorrectionSigma=`opts_DefaultOpt $CorrectionSigma $(echo "sqrt ( 200 )" | bc -l)`
-RegName=`opts_DefaultOpt $RegName FS`
+RegName=`opts_DefaultOpt $RegName MSMSulc`
 InflateExtraScale=`opts_DefaultOpt $InflateExtraScale 1`
+ProcessingMode=`opts_DefaultOpt $ProcessingMode "HCPStyleData"`
 
 PipelineScripts=${HCPPIPEDIR_PostFS}
 
+verbose_red_echo "---> Starting ${script_name}"
+verbose_echo " "
+verbose_echo " Using parameters ..."
+verbose_echo "              --path: ${StudyFolder}"
+verbose_echo "           --subject: ${Subject}"
+verbose_echo "      --surfatlasdir: ${SurfaceAtlasDIR}"
+verbose_echo "  --grayordinatesdir: ${GrayordinatesSpaceDIR}"
+verbose_echo "  --grayordinatesres: ${GrayordinatesResolutions}"
+verbose_echo "         --hiresmesh: ${HighResMesh}"
+verbose_echo "        --lowresmesh: ${LowResMeshes}"
+verbose_echo " --subcortgraylabels: ${SubcorticalGrayLabels}"
+verbose_echo "  --freesurferlabels: ${FreeSurferLabels}"
+verbose_echo "     --refmyelinmaps: ${ReferenceMyelinMaps}"
+verbose_echo "           --mcsigma: ${CorrectionSigma}"
+verbose_echo "           --regname: ${RegName}"
+verbose_echo "   --processing-mode: ${ProcessingMode}"
+verbose_echo ""
+verbose_echo " Using environment setting ..."
+verbose_echo "          HCPPIPEDIR: ${HCPPIPEDIR}"
+verbose_echo " "
+
 #Naming Conventions
 # Do NOT include spaces in any of these names
 T1wImage="T1w_acpc_dc"
@@ -141,6 +165,36 @@ FreeSurferFolder="$T1wFolder"/"$FreeSurferFolder"
 AtlasTransform="$AtlasSpaceFolder"/xfms/"$AtlasTransform"
 InverseAtlasTransform="$AtlasSpaceFolder"/xfms/"$InverseAtlasTransform"
 
+
+# ------------------------------------------------------------------------------
+#  Compliance check
+# ------------------------------------------------------------------------------
+
+Compliance="HCPStyleData"
+ComplianceMsg=""
+
+# -- T2w image
+
+if [ `${FSLDIR}/bin/imtest ${T2wFolder}/T2w` -eq 0 ]; then
+    ComplianceMsg+=" T2w image not present"
+    Compliance="LegacyStyleData"
+    T2wRestoreImage="NONE"
+fi
+
+if [ "${RegName}" = "FS" ] ; then
+    log_Warn "FreeSurfer's surface registration (based on cortical folding) is deprecated in the"
+    log_Warn "  HCP Pipelines as it results in poorer cross-subject functional and cortical areal "
+    log_Warn "  alignment relative to MSMSulc. Additionally, FreeSurfer registration results in "
+    log_Warn "  dramatically higher surface distortion (both isotropic and anisotropic). These things"
+    log_Warn "  occur because FreeSurfer's registration has too little regularization of folding patterns"
+    log_Warn "  that are imperfectly correlated with function and cortical areas, resulting in overfitting"
+    log_Warn "  of folding patterns. See Robinson et al 2014, 2018 Neuroimage, and Coalson et al 2018 PNAS"
+    log_Warn "  for more details."
+fi
+
+check_mode_compliance "${ProcessingMode}" "${Compliance}" "${ComplianceMsg}"
+
+
 #Conversion of FreeSurfer Volumes and Surfaces to NIFTI and GIFTI and Create Caret Files and Registration
 log_Msg "Conversion of FreeSurfer Volumes and Surfaces to NIFTI and GIFTI and Create Caret Files and Registration"
 log_Msg "RegName: ${RegName}"
@@ -184,7 +238,6 @@ argList+="$T1wRestoreImage "           # ${7}  Called T1wImage in CreateRibbon.s
 argList+="$FreeSurferLabels "          # ${8}
 "$PipelineScripts"/CreateRibbon.sh ${argList}
 
-
 #Myelin Mapping
 log_Msg "Myelin Mapping"
 log_Msg "RegName: ${RegName}"
@@ -230,4 +283,8 @@ argList+="$CorrectionSigma "
 argList+="$RegName "                                  # ${39}
 "$PipelineScripts"/CreateMyelinMaps.sh ${argList}
 
+verbose_green_echo "---> Finished ${script_name}"
+verbose_echo " "
+
 log_Msg "Completed"
+
diff --git a/PostFreeSurfer/PostFreeSurferPipeline_1res.sh b/PostFreeSurfer/PostFreeSurferPipeline_1res.sh
index 273b1d13c..423ba3077 100755
--- a/PostFreeSurfer/PostFreeSurferPipeline_1res.sh
+++ b/PostFreeSurfer/PostFreeSurferPipeline_1res.sh
@@ -12,17 +12,17 @@ set -e
 script_name=$(basename "${0}")
 
 if [ -z "${HCPPIPEDIR}" ]; then
-	echo "${script_name}: ABORTING: HCPPIPEDIR environment variable must be set"
-	exit 1
+  echo "${script_name}: ABORTING: HCPPIPEDIR environment variable must be set"
+  exit 1
 else
-	echo "${script_name}: HCPPIPEDIR: ${HCPPIPEDIR}"
+  echo "${script_name}: HCPPIPEDIR: ${HCPPIPEDIR}"
 fi
 
 if [ -z "${HCPPIPEDIR_PostFS}" ]; then
-	echo "${script_name}: ABORTING: HCPPIPEDIR_PostFS environment variable must be set"
-	exit 1
+  echo "${script_name}: ABORTING: HCPPIPEDIR_PostFS environment variable must be set"
+  exit 1
 else
-	echo "${script_name}: HCPPIPEDIR_PostFS: ${HCPPIPEDIR_PostFS}"
+  echo "${script_name}: HCPPIPEDIR_PostFS: ${HCPPIPEDIR_PostFS}"
 fi
 
 ########################################## PIPELINE OVERVIEW ##########################################
@@ -37,8 +37,9 @@ fi
 #  Load Function Libraries
 # --------------------------------------------------------------------------------
 
-source $HCPPIPEDIR/global/scripts/log.shlib  # Logging related functions
-source $HCPPIPEDIR/global/scripts/opts.shlib # Command line option functions
+source ${HCPPIPEDIR}/global/scripts/log.shlib   # Logging related functions
+source ${HCPPIPEDIR}/global/scripts/opts.shlib  # Command line option functions
+source ${HCPPIPEDIR}/global/scripts/processingmodecheck.shlib  # Checking processing mode compliance
 
 ########################################## SUPPORT FUNCTIONS ##########################################
 
@@ -80,15 +81,37 @@ ReferenceMyelinMaps=`opts_GetOpt1 "--refmyelinmaps" $@`
 CorrectionSigma=`opts_GetOpt1 "--mcsigma" $@`
 RegName=`opts_GetOpt1 "--regname" $@`
 InflateExtraScale=`opts_GetOpt1 "--inflatescale" $@`
+ProcessingMode=`opts_GetOpt1 "--processing-mode" $@`
 
 log_Msg "RegName: ${RegName}"
 # default parameters
 CorrectionSigma=`opts_DefaultOpt $CorrectionSigma $(echo "sqrt ( 200 )" | bc -l)`
-RegName=`opts_DefaultOpt $RegName FS`
+RegName=`opts_DefaultOpt $RegName MSMSulc`
 InflateExtraScale=`opts_DefaultOpt $InflateExtraScale 1`
+ProcessingMode=`opts_DefaultOpt $ProcessingMode "HCPStyleData"`
 
 PipelineScripts=${HCPPIPEDIR_PostFS}
 
+verbose_red_echo "---> Starting ${script_name}"
+verbose_echo " "
+verbose_echo " Using parameters ..."
+verbose_echo "              --path: ${StudyFolder}"
+verbose_echo "           --subject: ${Subject}"
+verbose_echo "      --surfatlasdir: ${SurfaceAtlasDIR}"
+verbose_echo "  --grayordinatesdir: ${GrayordinatesSpaceDIR}"
+verbose_echo "  --grayordinatesres: ${GrayordinatesResolutions}"
+verbose_echo "         --hiresmesh: ${HighResMesh}"
+verbose_echo "        --lowresmesh: ${LowResMeshes}"
+verbose_echo " --subcortgraylabels: ${SubcorticalGrayLabels}"
+verbose_echo "  --freesurferlabels: ${FreeSurferLabels}"
+verbose_echo "     --refmyelinmaps: ${ReferenceMyelinMaps}"
+verbose_echo "           --mcsigma: ${CorrectionSigma}"
+verbose_echo "           --regname: ${RegName}"
+verbose_echo "   --processing-mode: ${ProcessingMode}"
+verbose_echo " "
+verbose_echo " Using environment setting ..."
+verbose_echo "          HCPPIPEDIR: ${HCPPIPEDIR}"
+
 #Naming Conventions
 # Do NOT include spaces in any of these names
 T1wImage="T1w_acpc_dc"
@@ -140,6 +163,37 @@ FreeSurferFolder="$T1wFolder"/"$FreeSurferFolder"
 AtlasTransform="$AtlasSpaceFolder"/xfms/"$AtlasTransform"
 InverseAtlasTransform="$AtlasSpaceFolder"/xfms/"$InverseAtlasTransform"
 
+
+# ------------------------------------------------------------------------------
+#  Compliance check
+# ------------------------------------------------------------------------------
+
+Compliance="HCPStyleData"
+ComplianceMsg=""
+
+# -- T2w image
+
+if [ `${FSLDIR}/bin/imtest ${T2wFolder}/T2w` -eq 0 ]; then
+    ComplianceMsg+=" T2w image not present"
+    Compliance="LegacyStyleData"
+    T2wRestoreImage="NONE"
+fi
+
+if [ "${RegName}" = "FS" ] ; then
+    log_Warn "FreeSurfer's surface registration (based on cortical folding) is deprecated in the"
+    log_Warn "  HCP Pipelines as it results in poorer cross-subject functional and cortical areal "
+    log_Warn "  alignment relative to MSMSulc. Additionally, FreeSurfer registration results in "
+    log_Warn "  dramatically higher surface distortion (both isotropic and anisotropic). These things"
+    log_Warn "  occur because FreeSurfer's registration has too little regularization of folding patterns"
+    log_Warn "  that are imperfectly correlated with function and cortical areas, resulting in overfitting"
+    log_Warn "  of folding patterns. See Robinson et al 2014, 2018 Neuroimage, and Coalson et al 2018 PNAS"
+    log_Warn "  for more details."
+fi
+
+check_mode_compliance "${ProcessingMode}" "${Compliance}" "${ComplianceMsg}"
+
+
+
 #Conversion of FreeSurfer Volumes and Surfaces to NIFTI and GIFTI and Create Caret Files and Registration
 log_Msg "Conversion of FreeSurfer Volumes and Surfaces to NIFTI and GIFTI and Create Caret Files and Registration"
 log_Msg "RegName: ${RegName}"
@@ -215,4 +269,7 @@ argList+="$CorrectionSigma "
 argList+="$RegName "                                  # ${39}
 "$PipelineScripts"/CreateMyelinMaps_1res.sh ${argList}
 
+verbose_green_echo "---> Finished ${script_name}"
+verbose_echo " "
+
 log_Msg "Completed"
diff --git a/PostFreeSurfer/scripts/CreateMyelinMaps.sh b/PostFreeSurfer/scripts/CreateMyelinMaps.sh
index 897d42b89..284a4f026 100755
--- a/PostFreeSurfer/scripts/CreateMyelinMaps.sh
+++ b/PostFreeSurfer/scripts/CreateMyelinMaps.sh
@@ -65,6 +65,18 @@ RegName="${39}"
 
 log_Msg "CreateMyelinMaps.sh: RegName: ${RegName}"
 
+verbose_echo " "
+verbose_red_echo " ===> Running CreateMyelinMaps"
+verbose_echo " "
+
+# -- check for presence of T2w image
+if [ `${FSLDIR}/bin/imtest ${OrginalT2wImage}` -eq 0 ]; then
+  T2wPresent="NO"
+else
+  T2wPresent="YES"
+fi
+
+
 LeftGreyRibbonValue="3"
 RightGreyRibbonValue="42"
 MyelinMappingFWHM="5"
@@ -83,25 +95,25 @@ ${CARET7DIR}/wb_command -volume-palette $Jacobian MODE_AUTO_SCALE -interpolate t
 #     generated by FreeSurferPipeline.
 # [An implication of (2) is that FreeSurferPipeline should NOT be run using the T2w_acpc_dc.nii.gz output
 # by this script (CreateMyelinMaps) because then we'd lose this refinement in the T2wToT1w registration.
-# To detect this situation, and prevent it from occurring, FreeSurferPipeline errors out if the
-# one-step warpfield created here ($OutputOrigT2wToT1w) already exists.]
-convertwarp --relout --rel --ref="$T1wImageBrainMask" --premat="$InitialT1wTransform" --warp1="$dcT1wTransform" --out="$OutputOrigT1wToT1w"
-convertwarp --relout --rel --ref="$T1wImageBrainMask" --premat="$InitialT2wTransform" --warp1="$dcT2wTransform" --postmat="$FinalT2wTransform" --out="$OutputOrigT2wToT1w"
+# To detect this situation, and prevent FreeSurferPipeline from running after PostFreeSurferPipeline,
+# FreeSurferPipeline errors out if the one-step warpfield created here ($OutputOrigT1wToT1w) already exists.]
 
+convertwarp --relout --rel --ref="$T1wImageBrainMask" --premat="$InitialT1wTransform" --warp1="$dcT1wTransform" --out="$OutputOrigT1wToT1w"
 applywarp --rel --interp=spline -i "$OrginalT1wImage" -r "$T1wImageBrainMask" -w "$OutputOrigT1wToT1w" -o "$OutputT1wImage"
 fslmaths "$OutputT1wImage" -abs "$OutputT1wImage" -odt float
 fslmaths "$OutputT1wImage" -div "$BiasField" "$OutputT1wImageRestore"
 fslmaths "$OutputT1wImageRestore" -mas "$T1wImageBrainMask" "$OutputT1wImageRestoreBrain"
 
-applywarp --rel --interp=spline -i "$OrginalT2wImage" -r "$T1wImageBrainMask" -w "$OutputOrigT2wToT1w" -o "$OutputT2wImage"
-fslmaths "$OutputT2wImage" -abs "$OutputT2wImage" -odt float
-fslmaths "$OutputT2wImage" -div "$BiasField" "$OutputT2wImageRestore"
-fslmaths "$OutputT2wImageRestore" -mas "$T1wImageBrainMask" "$OutputT2wImageRestoreBrain"
+if [ "${T2wPresent}" = "YES" ] ; then
+  convertwarp --relout --rel --ref="$T1wImageBrainMask" --premat="$InitialT2wTransform" --warp1="$dcT2wTransform" --postmat="$FinalT2wTransform" --out="$OutputOrigT2wToT1w"
+  applywarp --rel --interp=spline -i "$OrginalT2wImage" -r "$T1wImageBrainMask" -w "$OutputOrigT2wToT1w" -o "$OutputT2wImage"
+  fslmaths "$OutputT2wImage" -abs "$OutputT2wImage" -odt float
+  fslmaths "$OutputT2wImage" -div "$BiasField" "$OutputT2wImageRestore"
+  fslmaths "$OutputT2wImageRestore" -mas "$T1wImageBrainMask" "$OutputT2wImageRestoreBrain"
+fi
 
 # Do the same for the equivalents in MNINonLinear space
 convertwarp --relout --rel --ref="$T1wImageBrainMask" --warp1="$OutputOrigT1wToT1w" --warp2="$AtlasTransform" --out="$OutputOrigT1wToStandard"
-convertwarp --relout --rel --ref="$T1wImageBrainMask" --warp1="$OutputOrigT2wToT1w" --warp2="$AtlasTransform" --out="$OutputOrigT2wToStandard"
-
 applywarp --rel --interp=spline -i "$BiasField" -r "$T1wImageBrainMask" -w "$AtlasTransform" -o "$BiasFieldOutput"
 fslmaths "$BiasFieldOutput" -thr 0.1 "$BiasFieldOutput"
 
@@ -110,20 +122,31 @@ fslmaths "$OutputMNIT1wImage" -abs "$OutputMNIT1wImage" -odt float
 fslmaths "$OutputMNIT1wImage" -div "$BiasFieldOutput" "$OutputMNIT1wImageRestore"
 fslmaths "$OutputMNIT1wImageRestore" -mas "$T1wMNIImageBrainMask" "$OutputMNIT1wImageRestoreBrain"
 
-applywarp --rel --interp=spline -i "$OrginalT2wImage" -r "$T1wImageBrainMask" -w "$OutputOrigT2wToStandard" -o "$OutputMNIT2wImage"
-fslmaths "$OutputMNIT2wImage" -abs "$OutputMNIT2wImage" -odt float
-fslmaths "$OutputMNIT2wImage" -div "$BiasFieldOutput" "$OutputMNIT2wImageRestore"
-fslmaths "$OutputMNIT2wImageRestore" -mas "$T1wMNIImageBrainMask" "$OutputMNIT2wImageRestoreBrain"
+if [ "${T2wPresent}" = "YES" ] ; then
+  convertwarp --relout --rel --ref="$T1wImageBrainMask" --warp1="$OutputOrigT2wToT1w" --warp2="$AtlasTransform" --out="$OutputOrigT2wToStandard"
+  applywarp --rel --interp=spline -i "$OrginalT2wImage" -r "$T1wImageBrainMask" -w "$OutputOrigT2wToStandard" -o "$OutputMNIT2wImage"
+  fslmaths "$OutputMNIT2wImage" -abs "$OutputMNIT2wImage" -odt float
+  fslmaths "$OutputMNIT2wImage" -div "$BiasFieldOutput" "$OutputMNIT2wImageRestore"
+  fslmaths "$OutputMNIT2wImageRestore" -mas "$T1wMNIImageBrainMask" "$OutputMNIT2wImageRestoreBrain"
+fi
 
 # Create T1w/T2w maps
-${CARET7DIR}/wb_command -volume-math "clamp((T1w / T2w), 0, 100)" "$T1wFolder"/T1wDividedByT2w.nii.gz -var T1w "$OutputT1wImage".nii.gz -var T2w "$OutputT2wImage".nii.gz -fixnan 0
-${CARET7DIR}/wb_command -volume-palette "$T1wFolder"/T1wDividedByT2w.nii.gz MODE_AUTO_SCALE_PERCENTAGE -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
-${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$T1wFolder"/T1wDividedByT2w.nii.gz
-${CARET7DIR}/wb_command -volume-math "(T1w / T2w) * (((ribbon > ($LeftGreyRibbonValue - 0.01)) * (ribbon < ($LeftGreyRibbonValue + 0.01))) + ((ribbon > ($RightGreyRibbonValue - 0.01)) * (ribbon < ($RightGreyRibbonValue + 0.01))))" "$T1wFolder"/T1wDividedByT2w_ribbon.nii.gz -var T1w "$OutputT1wImage".nii.gz -var T2w "$OutputT2wImage".nii.gz -var ribbon "$T1wFolder"/ribbon.nii.gz
-${CARET7DIR}/wb_command -volume-palette "$T1wFolder"/T1wDividedByT2w_ribbon.nii.gz MODE_AUTO_SCALE_PERCENTAGE -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
-${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$T1wFolder"/T1wDividedByT2w_ribbon.nii.gz
+if [ "${T2wPresent}" = "YES" ] ; then  
+  ${CARET7DIR}/wb_command -volume-math "clamp((T1w / T2w), 0, 100)" "$T1wFolder"/T1wDividedByT2w.nii.gz -var T1w "$OutputT1wImage".nii.gz -var T2w "$OutputT2wImage".nii.gz -fixnan 0
+  ${CARET7DIR}/wb_command -volume-palette "$T1wFolder"/T1wDividedByT2w.nii.gz MODE_AUTO_SCALE_PERCENTAGE -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
+  ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$T1wFolder"/T1wDividedByT2w.nii.gz
+  ${CARET7DIR}/wb_command -volume-math "(T1w / T2w) * (((ribbon > ($LeftGreyRibbonValue - 0.01)) * (ribbon < ($LeftGreyRibbonValue + 0.01))) + ((ribbon > ($RightGreyRibbonValue - 0.01)) * (ribbon < ($RightGreyRibbonValue + 0.01))))" "$T1wFolder"/T1wDividedByT2w_ribbon.nii.gz -var T1w "$OutputT1wImage".nii.gz -var T2w "$OutputT2wImage".nii.gz -var ribbon "$T1wFolder"/ribbon.nii.gz
+  ${CARET7DIR}/wb_command -volume-palette "$T1wFolder"/T1wDividedByT2w_ribbon.nii.gz MODE_AUTO_SCALE_PERCENTAGE -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
+  ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$T1wFolder"/T1wDividedByT2w_ribbon.nii.gz
+
+  ${CARET7DIR}/wb_command -cifti-separate-all "$ReferenceMyelinMaps" -left "$AtlasSpaceFolder"/"$Subject".L.RefMyelinMap."$HighResMesh"k_fs_LR.func.gii -right "$AtlasSpaceFolder"/"$Subject".R.RefMyelinMap."$HighResMesh"k_fs_LR.func.gii
+fi
+
 
-${CARET7DIR}/wb_command -cifti-separate-all "$ReferenceMyelinMaps" -left "$AtlasSpaceFolder"/"$Subject".L.RefMyelinMap."$HighResMesh"k_fs_LR.func.gii -right "$AtlasSpaceFolder"/"$Subject".R.RefMyelinMap."$HighResMesh"k_fs_LR.func.gii
+STRINGList="corrThickness@shape"
+if [ "${T2wPresent}" = "YES" ] ; then
+  STRINGList+=" MyelinMap@func SmoothedMyelinMap@func MyelinMap_BC@func SmoothedMyelinMap_BC@func"
+fi
 
 for Hemisphere in L R ; do
   if [ $Hemisphere = "L" ] ; then
@@ -139,34 +162,38 @@ for Hemisphere in L R ; do
     RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii"
   fi
 
-  ${CARET7DIR}/wb_command -volume-math "(ribbon > ($ribbon - 0.01)) * (ribbon < ($ribbon + 0.01))" "$T1wFolder"/temp_ribbon.nii.gz -var ribbon "$T1wFolder"/ribbon.nii.gz
-  ${CARET7DIR}/wb_command -volume-to-surface-mapping "$T1wFolder"/T1wDividedByT2w.nii.gz "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap.native.func.gii -myelin-style "$T1wFolder"/temp_ribbon.nii.gz "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$MyelinMappingSigma"
-  rm "$T1wFolder"/temp_ribbon.nii.gz
   ${CARET7DIR}/wb_command -metric-regression "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".corrThickness.native.shape.gii -roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -remove "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii
-  ${CARET7DIR}/wb_command -metric-smoothing "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap.native.func.gii "$SurfaceSmoothingSigma" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".SmoothedMyelinMap.native.func.gii -roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-
-  ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".RefMyelinMap."$HighResMesh"k_fs_LR.func.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ${RegSphere} ADAP_BARY_AREA "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii -area-surfs "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii -current-roi "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii
-  ${CARET7DIR}/wb_command -metric-dilate "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 30 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii -nearest
-  ${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii
 
   #Reduce memory usage by smoothing on downsampled mesh
   LowResMesh=`echo ${LowResMeshes} | cut -d " " -f 1`
-  for Map in MyelinMap RefMyelinMap ; do
-    ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.func.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.func.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii -current-roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-    ${CARET7DIR}/wb_command -metric-smoothing "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.func.gii "$CorrectionSigma" "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma"."$LowResMesh"k_fs_LR.func.gii -roi "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii
-    ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma"."$LowResMesh"k_fs_LR.func.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ${RegSphere} ADAP_BARY_AREA "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma".native.func.gii -area-surfs "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii -current-roi "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii
-    ${CARET7DIR}/wb_command -metric-dilate "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma".native.func.gii "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 30 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma".native.func.gii -nearest
-    ${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma".native.func.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma".native.func.gii
-    rm "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.func.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma"."$LowResMesh"k_fs_LR.func.gii
-  done
-  #${CARET7DIR}/wb_command -metric-smoothing "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap.native.func.gii "$CorrectionSigma" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap_s"$CorrectionSigma".native.func.gii -roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-  #${CARET7DIR}/wb_command -metric-smoothing "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii "$CorrectionSigma" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap_s"$CorrectionSigma".native.func.gii -roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-
-  ${CARET7DIR}/wb_command -metric-math "(Individual - Reference) * Mask" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".BiasField.native.func.gii -var Individual "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap_s"$CorrectionSigma".native.func.gii -var Reference "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap_s"$CorrectionSigma".native.func.gii -var Mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-  ${CARET7DIR}/wb_command -metric-math "(Individual - Bias) * Mask" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap_BC.native.func.gii -var Individual "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap.native.func.gii -var Bias "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".BiasField.native.func.gii -var Mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-  ${CARET7DIR}/wb_command -metric-math "(Individual - Bias) * Mask" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".SmoothedMyelinMap_BC.native.func.gii -var Individual "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".SmoothedMyelinMap.native.func.gii -var Bias "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".BiasField.native.func.gii -var Mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-  rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap_s"$CorrectionSigma".native.func.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap_s"$CorrectionSigma".native.func.gii
-  for STRING in MyelinMap@func SmoothedMyelinMap@func MyelinMap_BC@func SmoothedMyelinMap_BC@func corrThickness@shape ; do
+  
+  if [ "${T2wPresent}" = "YES" ] ; then
+    ${CARET7DIR}/wb_command -volume-math "(ribbon > ($ribbon - 0.01)) * (ribbon < ($ribbon + 0.01))" "$T1wFolder"/temp_ribbon.nii.gz -var ribbon "$T1wFolder"/ribbon.nii.gz
+    ${CARET7DIR}/wb_command -volume-to-surface-mapping "$T1wFolder"/T1wDividedByT2w.nii.gz "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap.native.func.gii -myelin-style "$T1wFolder"/temp_ribbon.nii.gz "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$MyelinMappingSigma"
+    rm "$T1wFolder"/temp_ribbon.nii.gz
+    ${CARET7DIR}/wb_command -metric-smoothing "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap.native.func.gii "$SurfaceSmoothingSigma" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".SmoothedMyelinMap.native.func.gii -roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii  
+    ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".RefMyelinMap."$HighResMesh"k_fs_LR.func.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ${RegSphere} ADAP_BARY_AREA "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii -area-surfs "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii -current-roi "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii
+    ${CARET7DIR}/wb_command -metric-dilate "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 30 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii -nearest
+    ${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii
+
+    for Map in MyelinMap RefMyelinMap ; do
+      ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.func.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.func.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii -current-roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+      ${CARET7DIR}/wb_command -metric-smoothing "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.func.gii "$CorrectionSigma" "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma"."$LowResMesh"k_fs_LR.func.gii -roi "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii
+      ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma"."$LowResMesh"k_fs_LR.func.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ${RegSphere} ADAP_BARY_AREA "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma".native.func.gii -area-surfs "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii -current-roi "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii
+      ${CARET7DIR}/wb_command -metric-dilate "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma".native.func.gii "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 30 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma".native.func.gii -nearest
+      ${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma".native.func.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma".native.func.gii
+      rm "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.func.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"_s"$CorrectionSigma"."$LowResMesh"k_fs_LR.func.gii
+    done
+    #${CARET7DIR}/wb_command -metric-smoothing "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap.native.func.gii "$CorrectionSigma" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap_s"$CorrectionSigma".native.func.gii -roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+    #${CARET7DIR}/wb_command -metric-smoothing "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap.native.func.gii "$CorrectionSigma" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap_s"$CorrectionSigma".native.func.gii -roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+
+    ${CARET7DIR}/wb_command -metric-math "(Individual - Reference) * Mask" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".BiasField.native.func.gii -var Individual "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap_s"$CorrectionSigma".native.func.gii -var Reference "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap_s"$CorrectionSigma".native.func.gii -var Mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+    ${CARET7DIR}/wb_command -metric-math "(Individual - Bias) * Mask" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap_BC.native.func.gii -var Individual "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap.native.func.gii -var Bias "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".BiasField.native.func.gii -var Mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+    ${CARET7DIR}/wb_command -metric-math "(Individual - Bias) * Mask" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".SmoothedMyelinMap_BC.native.func.gii -var Individual "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".SmoothedMyelinMap.native.func.gii -var Bias "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".BiasField.native.func.gii -var Mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+    rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".MyelinMap_s"$CorrectionSigma".native.func.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".RefMyelinMap_s"$CorrectionSigma".native.func.gii
+  fi
+
+  for STRING in $STRINGList ; do
     Map=`echo $STRING | cut -d "@" -f 1`
     Ext=`echo $STRING | cut -d "@" -f 2`
     ${CARET7DIR}/wb_command -set-map-name "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native."$Ext".gii 1 "$Subject"_"$Hemisphere"_"$Map"
@@ -190,7 +217,8 @@ for STRING in "$AtlasSpaceFolder"/"$NativeFolder"@native@roi "$AtlasSpaceFolder"
   Folder=`echo $STRING | cut -d "@" -f 1`
   Mesh=`echo $STRING | cut -d "@" -f 2`
   ROI=`echo $STRING | cut -d "@" -f 3`
-  for STRINGII in MyelinMap@func SmoothedMyelinMap@func MyelinMap_BC@func SmoothedMyelinMap_BC@func corrThickness@shape ; do
+
+  for STRINGII in $STRINGList ; do
     Map=`echo $STRINGII | cut -d "@" -f 1`
     Ext=`echo $STRINGII | cut -d "@" -f 2`
     ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".${Map}."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.${Map}."$Mesh"."$Ext".gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.${Map}."$Mesh"."$Ext".gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
@@ -205,15 +233,24 @@ for LowResMesh in ${LowResMeshes} ; do
 done
 
 #Add CIFTI Maps to Spec Files
+STRINGIIList="corrThickness@dscalar"
+if [ "${T2wPresent}" = "YES" ] ; then
+  STRINGIIList+=" MyelinMap_BC@dscalar SmoothedMyelinMap_BC@dscalar"
+fi
+
 for STRING in "$T1wFolder"/"$NativeFolder"@"$AtlasSpaceFolder"/"$NativeFolder"@native "$AtlasSpaceFolder"/"$NativeFolder"@"$AtlasSpaceFolder"/"$NativeFolder"@native "$AtlasSpaceFolder"@"$AtlasSpaceFolder"@"$HighResMesh"k_fs_LR ${STRINGII} ; do
   FolderI=`echo $STRING | cut -d "@" -f 1`
   FolderII=`echo $STRING | cut -d "@" -f 2`
   Mesh=`echo $STRING | cut -d "@" -f 3`
-  for STRINGII in MyelinMap_BC@dscalar SmoothedMyelinMap_BC@dscalar corrThickness@dscalar ; do
+
+  for STRINGII in $STRINGIIList ; do
     Map=`echo $STRINGII | cut -d "@" -f 1`
     Ext=`echo $STRINGII | cut -d "@" -f 2`
     ${CARET7DIR}/wb_command -add-to-spec-file "$FolderI"/"$Subject"."$Mesh".wb.spec INVALID "$FolderII"/"$Subject"."$Map"."$Mesh"."$Ext".nii
   done
 done
 
+verbose_green_echo "---> Finished CreateMyelinMaps"
+verbose_echo " "
+
 log_Msg "END: CreateMyelinMaps"
diff --git a/PostFreeSurfer/scripts/CreateMyelinMaps_1res.sh b/PostFreeSurfer/scripts/CreateMyelinMaps_1res.sh
index 6c3231627..38dfd80d3 100755
--- a/PostFreeSurfer/scripts/CreateMyelinMaps_1res.sh
+++ b/PostFreeSurfer/scripts/CreateMyelinMaps_1res.sh
@@ -64,6 +64,18 @@ CorrectionSigma="${38}"
 RegName="${39}"
 
 log_Msg "CreateMyelinMaps_1res.sh: RegName: ${RegName}"
+
+verbose_echo " "
+verbose_red_echo " ===> Running CreateMyelinMaps_1res"
+verbose_echo " "
+
+# -- check for presence of T2w image
+if [ `${FSLDIR}/bin/imtest ${OrginalT2wImage}` -eq 0 ]; then
+  T2wPresent="NO"
+else
+  T2wPresent="YES"
+fi
+
 LeftGreyRibbonValue="3"
 RightGreyRibbonValue="42"
 MyelinMappingFWHM="5"
@@ -73,6 +85,11 @@ SurfaceSmoothingSigma=`echo "$SurfaceSmoothingFWHM / ( 2 * ( sqrt ( 2 * l ( 2 )
 
 LowResMeshes=`echo ${LowResMeshes} | sed 's/@/ /g'`
 
+STRINGList="corrThickness@shape"
+if [ "${T2wPresent}" = "YES" ] ; then
+  STRINGList+=" MyelinMap@func SmoothedMyelinMap@func MyelinMap_BC@func SmoothedMyelinMap_BC@func"
+fi
+
 for Hemisphere in L R ; do
   if [ $Hemisphere = "L" ] ; then
     Structure="CORTEX_LEFT"
@@ -87,7 +104,7 @@ for Hemisphere in L R ; do
     RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii"
   fi
 
-  for STRING in MyelinMap@func SmoothedMyelinMap@func MyelinMap_BC@func SmoothedMyelinMap_BC@func corrThickness@shape ; do
+  for STRING in $STRINGList ; do
     Map=`echo $STRING | cut -d "@" -f 1`
     Ext=`echo $STRING | cut -d "@" -f 2`
 
@@ -108,7 +125,8 @@ for STRING in ${STRINGII} ; do
   Folder=`echo $STRING | cut -d "@" -f 1`
   Mesh=`echo $STRING | cut -d "@" -f 2`
   ROI=`echo $STRING | cut -d "@" -f 3`
-  for STRINGII in MyelinMap@func SmoothedMyelinMap@func MyelinMap_BC@func SmoothedMyelinMap_BC@func corrThickness@shape ; do
+
+  for STRINGII in $STRINGList ; do
     Map=`echo $STRINGII | cut -d "@" -f 1`
     Ext=`echo $STRINGII | cut -d "@" -f 2`
     ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".${Map}."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.${Map}."$Mesh"."$Ext".gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.${Map}."$Mesh"."$Ext".gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
@@ -123,15 +141,25 @@ for LowResMesh in ${LowResMeshes} ; do
 done
 
 #Add CIFTI Maps to Spec Files
+
+STRINGIIList="corrThickness@dscalar"
+if [ "${T2wPresent}" = "YES" ] ; then
+  STRINGIIList+=" MyelinMap_BC@dscalar SmoothedMyelinMap_BC@dscalar"
+fi
+  
 for STRING in ${STRINGII} ; do
   FolderI=`echo $STRING | cut -d "@" -f 1`
   FolderII=`echo $STRING | cut -d "@" -f 2`
   Mesh=`echo $STRING | cut -d "@" -f 3`
-  for STRINGII in MyelinMap_BC@dscalar SmoothedMyelinMap_BC@dscalar corrThickness@dscalar ; do
+
+  for STRINGII in $STRINGIIList ; do
     Map=`echo $STRINGII | cut -d "@" -f 1`
     Ext=`echo $STRINGII | cut -d "@" -f 2`
     ${CARET7DIR}/wb_command -add-to-spec-file "$FolderI"/"$Subject"."$Mesh".wb.spec INVALID "$FolderII"/"$Subject"."$Map"."$Mesh"."$Ext".nii
   done
 done
 
+verbose_green_echo "---> Finished CreateMyelinMaps_1res"
+verbose_echo " "
+
 log_Msg "END: CreateMyelinMaps_1res"
diff --git a/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh b/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh
index b762954a2..316cd2779 100755
--- a/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh
+++ b/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh
@@ -6,10 +6,10 @@ set -e
 # ------------------------------------------------------------------------------
 
 if [ -z "${HCPPIPEDIR}" ]; then
-	echo "$(basename ${0}): ABORTING: HCPPIPEDIR environment variable must be set"
-	exit 1
+    echo "$(basename ${0}): ABORTING: HCPPIPEDIR environment variable must be set"
+    exit 1
 else
-	echo "$(basename ${0}): HCPPIPEDIR: ${HCPPIPEDIR}"
+    echo "$(basename ${0}): HCPPIPEDIR: ${HCPPIPEDIR}"
 fi
 
 # ------------------------------------------------------------------------------
@@ -23,21 +23,21 @@ source ${HCPPIPEDIR}/global/scripts/log.shlib # Logging related functions
 # ------------------------------------------------------------------------------
 
 if [ -z "${MSMBINDIR}" ]; then
-	log_Err_Abort "MSMBINDIR environment variable must be set"
+    log_Err_Abort "MSMBINDIR environment variable must be set"
 else
-	log_Msg "MSMBINDIR: ${MSMBINDIR}"
+    log_Msg "MSMBINDIR: ${MSMBINDIR}"
 fi
 
 if [ -z "${MSMCONFIGDIR}" ]; then
-	log_Err_Abort "MSMCONFIGDIR environment variable must be set"
+    log_Err_Abort "MSMCONFIGDIR environment variable must be set"
 else
-	log_Msg "MSMCONFIGDIR: ${MSMCONFIGDIR}"
+    log_Msg "MSMCONFIGDIR: ${MSMCONFIGDIR}"
 fi
 
 if [ -z "${CARET7DIR}" ]; then
-	log_Err_Abort "CARET7DIR environment variable must be set"
+    log_Err_Abort "CARET7DIR environment variable must be set"
 else
-	log_Msg "CARET7DIR: ${CARET7DIR}"
+    log_Msg "CARET7DIR: ${CARET7DIR}"
 fi
 
 # ------------------------------------------------------------------------------
@@ -123,47 +123,49 @@ log_Msg "GrayordinatesResolutions: ${GrayordinatesResolutions}"
 
 #Make some folders for this and later scripts
 if [ ! -e "$T1wFolder"/"$NativeFolder" ] ; then
-	mkdir -p "$T1wFolder"/"$NativeFolder"
+    mkdir -p "$T1wFolder"/"$NativeFolder"
 fi
 if [ ! -e "$AtlasSpaceFolder"/ROIs ] ; then
-	mkdir -p "$AtlasSpaceFolder"/ROIs
+    mkdir -p "$AtlasSpaceFolder"/ROIs
 fi
 if [ ! -e "$AtlasSpaceFolder"/Results ] ; then
-	mkdir "$AtlasSpaceFolder"/Results
+    mkdir "$AtlasSpaceFolder"/Results
 fi
 if [ ! -e "$AtlasSpaceFolder"/"$NativeFolder" ] ; then
-	mkdir "$AtlasSpaceFolder"/"$NativeFolder"
+    mkdir "$AtlasSpaceFolder"/"$NativeFolder"
 fi
 if [ ! -e "$AtlasSpaceFolder"/fsaverage ] ; then
-	mkdir "$AtlasSpaceFolder"/fsaverage
+    mkdir "$AtlasSpaceFolder"/fsaverage
 fi
 for LowResMesh in ${LowResMeshes} ; do
-	if [ ! -e "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k ] ; then
-		mkdir "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k
-	fi
-	if [ ! -e "$T1wFolder"/fsaverage_LR"$LowResMesh"k ] ; then
-		mkdir "$T1wFolder"/fsaverage_LR"$LowResMesh"k
-	fi
+    if [ ! -e "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k ] ; then
+        mkdir "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k
+    fi
+    if [ ! -e "$T1wFolder"/fsaverage_LR"$LowResMesh"k ] ; then
+        mkdir "$T1wFolder"/fsaverage_LR"$LowResMesh"k
+    fi
 done
 
-#Find c_ras offset between FreeSurfer surface and volume and generate matrix to transform surfaces
-MatrixX=$(mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_r" | cut -d "=" -f 5 | sed s/" "/""/g)
-MatrixY=$(mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_a" | cut -d "=" -f 5 | sed s/" "/""/g)
-MatrixZ=$(mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_s" | cut -d "=" -f 5 | sed s/" "/""/g)
-echo "1 0 0 ""$MatrixX" > "$FreeSurferFolder"/mri/c_ras.mat
-echo "0 1 0 ""$MatrixY" >> "$FreeSurferFolder"/mri/c_ras.mat
-echo "0 0 1 ""$MatrixZ" >> "$FreeSurferFolder"/mri/c_ras.mat
-echo "0 0 0 1" >> "$FreeSurferFolder"/mri/c_ras.mat
+# Find c_ras offset between FreeSurfer surface and volume and generate matrix to transform surfaces
+# -- Corrected code using native mri_info --cras function to build the needed variables
+MatrixXYZ=`mri_info --cras ${FreeSurferFolder}/mri/brain.finalsurfs.mgz`
+MatrixX=`echo ${MatrixXYZ} | awk '{print $1;}'`
+MatrixY=`echo ${MatrixXYZ} | awk '{print $2;}'`
+MatrixZ=`echo ${MatrixXYZ} | awk '{print $3;}'`
+echo "1 0 0 ${MatrixX}" >  ${FreeSurferFolder}/mri/c_ras.mat
+echo "0 1 0 ${MatrixY}" >> ${FreeSurferFolder}/mri/c_ras.mat
+echo "0 0 1 ${MatrixZ}" >> ${FreeSurferFolder}/mri/c_ras.mat
+echo "0 0 0 1"          >> ${FreeSurferFolder}/mri/c_ras.mat
 
 #Convert FreeSurfer Volumes
 for Image in wmparc aparc.a2009s+aseg aparc+aseg ; do
-	if [ -e "$FreeSurferFolder"/mri/"$Image".mgz ] ; then
-		mri_convert -rt nearest -rl "$T1wFolder"/"$T1wImage".nii.gz "$FreeSurferFolder"/mri/"$Image".mgz "$T1wFolder"/"$Image"_1mm.nii.gz
-		applywarp --rel --interp=nn -i "$T1wFolder"/"$Image"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage" --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wFolder"/"$Image".nii.gz
-		applywarp --rel --interp=nn -i "$T1wFolder"/"$Image"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage" -w "$AtlasTransform" -o "$AtlasSpaceFolder"/"$Image".nii.gz
-		${CARET7DIR}/wb_command -volume-label-import "$T1wFolder"/"$Image".nii.gz "$FreeSurferLabels" "$T1wFolder"/"$Image".nii.gz -drop-unused-labels
-		${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/"$Image".nii.gz "$FreeSurferLabels" "$AtlasSpaceFolder"/"$Image".nii.gz -drop-unused-labels
-	fi
+    if [ -e "$FreeSurferFolder"/mri/"$Image".mgz ] ; then
+        mri_convert -rt nearest -rl "$T1wFolder"/"$T1wImage".nii.gz "$FreeSurferFolder"/mri/"$Image".mgz "$T1wFolder"/"$Image"_1mm.nii.gz
+        applywarp --rel --interp=nn -i "$T1wFolder"/"$Image"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage" --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wFolder"/"$Image".nii.gz
+        applywarp --rel --interp=nn -i "$T1wFolder"/"$Image"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage" -w "$AtlasTransform" -o "$AtlasSpaceFolder"/"$Image".nii.gz
+        ${CARET7DIR}/wb_command -volume-label-import "$T1wFolder"/"$Image".nii.gz "$FreeSurferLabels" "$T1wFolder"/"$Image".nii.gz -drop-unused-labels
+        ${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/"$Image".nii.gz "$FreeSurferLabels" "$AtlasSpaceFolder"/"$Image".nii.gz -drop-unused-labels
+    fi
 done
 
 #Create FreeSurfer Brain Mask
@@ -174,384 +176,385 @@ applywarp --rel --interp=nn -i "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz -r "
 applywarp --rel --interp=nn -i "$T1wFolder"/"$T1wImageBrainMask"_1mm.nii.gz -r "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage" -w "$AtlasTransform" -o "$AtlasSpaceFolder"/"$T1wImageBrainMask".nii.gz
 
 #Add volume files to spec files
-${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$T1wFolder"/"$T2wImage".nii.gz
+
+[ "${T2wImage}" != "NONE" ] && ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$T1wFolder"/"$T2wImage".nii.gz
 ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$T1wFolder"/"$T1wImage".nii.gz
 
-${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
+[ "${T2wImage}" != "NONE" ] && ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
 ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage".nii.gz
 
-${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
+[ "${T2wImage}" != "NONE" ] && ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
 ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage".nii.gz
 
 for LowResMesh in ${LowResMeshes} ; do
-	${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
-	${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage".nii.gz
+  [ "${T2wImage}" != "NONE" ] && ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
+  ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage".nii.gz
 
-	${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$T1wFolder"/"$T2wImage".nii.gz
-	${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$T1wFolder"/"$T1wImage".nii.gz
+  [ "${T2wImage}" != "NONE" ] && ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$T1wFolder"/"$T2wImage".nii.gz
+  ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$T1wFolder"/"$T1wImage".nii.gz
 done
 
 #Import Subcortical ROIs
 for GrayordinatesResolution in ${GrayordinatesResolutions} ; do
-	cp "$GrayordinatesSpaceDIR"/Atlas_ROIs."$GrayordinatesResolution".nii.gz "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz
-	applywarp --interp=nn -i "$AtlasSpaceFolder"/wmparc.nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz
-	${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz "$FreeSurferLabels" "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz -drop-unused-labels
-	applywarp --interp=nn -i "$SurfaceAtlasDIR"/Avgwmparc.nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz
-	${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz "$FreeSurferLabels" "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz -drop-unused-labels
-	${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz ${SubcorticalGrayLabels} "$AtlasSpaceFolder"/ROIs/ROIs."$GrayordinatesResolution".nii.gz -discard-others
-	applywarp --interp=spline -i "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage"."$GrayordinatesResolution".nii.gz
-	applywarp --interp=spline -i "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage"."$GrayordinatesResolution".nii.gz
+    cp "$GrayordinatesSpaceDIR"/Atlas_ROIs."$GrayordinatesResolution".nii.gz "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz
+    applywarp --interp=nn -i "$AtlasSpaceFolder"/wmparc.nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz
+    ${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz "$FreeSurferLabels" "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz -drop-unused-labels
+    applywarp --interp=nn -i "$SurfaceAtlasDIR"/Avgwmparc.nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz
+    ${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz "$FreeSurferLabels" "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz -drop-unused-labels
+    ${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz ${SubcorticalGrayLabels} "$AtlasSpaceFolder"/ROIs/ROIs."$GrayordinatesResolution".nii.gz -discard-others
+    [ "${T2wImage}" != "NONE" ] && applywarp --interp=spline -i "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage"."$GrayordinatesResolution".nii.gz
+    applywarp --interp=spline -i "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage"."$GrayordinatesResolution".nii.gz
 done
 
 #Loop through left and right hemispheres
 for Hemisphere in L R ; do
-	#Set a bunch of different ways of saying left and right
-	if [ $Hemisphere = "L" ] ; then
-		hemisphere="l"
-		Structure="CORTEX_LEFT"
-	elif [ $Hemisphere = "R" ] ; then
-		hemisphere="r"
-		Structure="CORTEX_RIGHT"
-	fi
-
-	#native Mesh Processing
-	#Convert and volumetrically register white and pial surfaces makign linear and nonlinear copies, add each to the appropriate spec file
-	Types="ANATOMICAL@GRAY_WHITE ANATOMICAL@PIAL"
-	i=1
-	for Surface in white pial ; do
-		Type=$(echo "$Types" | cut -d " " -f $i)
-		Secondary=$(echo "$Type" | cut -d "@" -f 2)
-		Type=$(echo "$Type" | cut -d "@" -f 1)
-		if [ ! $Secondary = $Type ] ; then
-			Secondary=$(echo " -surface-secondary-type ""$Secondary")
-		else
-			Secondary=""
-		fi
-		mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$Surface" "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
-		${CARET7DIR}/wb_command -set-structure "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type $Type$Secondary
-		${CARET7DIR}/wb_command -surface-apply-affine "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii "$FreeSurferFolder"/mri/c_ras.mat "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
-		${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
-		${CARET7DIR}/wb_command -surface-apply-warpfield "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii "$InverseAtlasTransform".nii.gz "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii -fnirt "$AtlasTransform".nii.gz
-		${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
-		i=$(( i+1 ))
-	done
-
-	#Create midthickness by averaging white and pial surfaces and use it to make inflated surfacess
-	for Folder in "$T1wFolder" "$AtlasSpaceFolder" ; do
-		${CARET7DIR}/wb_command -surface-average "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii -surf "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".white.native.surf.gii -surf "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".pial.native.surf.gii
-		${CARET7DIR}/wb_command -set-structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii ${Structure} -surface-type ANATOMICAL -surface-secondary-type MIDTHICKNESS
-		${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii
-
-		#get number of vertices from native file
-		NativeVerts=$(${CARET7DIR}/wb_command -file-information "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii | grep 'Number of Vertices:' | cut -f2 -d: | tr -d '[:space:]')
-
-		#HCP fsaverage_LR32k used -iterations-scale 0.75. Compute new param value for native mesh density
-		NativeInflationScale=$(echo "scale=4; $InflateExtraScale * 0.75 * $NativeVerts / 32492" | bc -l)
-
-		${CARET7DIR}/wb_command -surface-generate-inflated "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".inflated.native.surf.gii "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".very_inflated.native.surf.gii -iterations-scale $NativeInflationScale
-		${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".inflated.native.surf.gii
-		${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".very_inflated.native.surf.gii
-	done
-
-	#Convert original and registered spherical surfaces and add them to the nonlinear spec file
-	for Surface in sphere.reg sphere ; do
-		mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$Surface" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
-		${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type SPHERICAL
-	done
-	${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii
-
-	#Add more files to the spec file and convert other FreeSurfer surface data to metric/GIFTI including sulc, curv, and thickness.
-	for Map in sulc@sulc@Sulc thickness@thickness@Thickness curv@curvature@Curvature ; do
-		fsname=$(echo $Map | cut -d "@" -f 1)
-		wbname=$(echo $Map | cut -d "@" -f 2)
-		mapname=$(echo $Map | cut -d "@" -f 3)
-		mris_convert -c "$FreeSurferFolder"/surf/"$hemisphere"h."$fsname" "$FreeSurferFolder"/surf/"$hemisphere"h.white "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii
-		${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii ${Structure}
-		${CARET7DIR}/wb_command -metric-math "var * -1" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii
-		${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii -map 1 "$Subject"_"$Hemisphere"_"$mapname"
-		${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii MODE_AUTO_SCALE_PERCENTAGE -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
-	done
-	#Thickness specific operations
-	${CARET7DIR}/wb_command -metric-math "abs(thickness)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii -var thickness "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
-	${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii MODE_AUTO_SCALE_PERCENTAGE -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
-	${CARET7DIR}/wb_command -metric-math "thickness > 0" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var thickness "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
-	${CARET7DIR}/wb_command -metric-fill-holes "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-	${CARET7DIR}/wb_command -metric-remove-islands "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-	${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_ROI
-	${CARET7DIR}/wb_command -metric-dilate "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 10 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii -nearest
-	${CARET7DIR}/wb_command -metric-dilate "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 10 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii -nearest
-
-	#Label operations
-	for Map in aparc aparc.a2009s ; do #Remove BA because it doesn't convert properly
-		if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
-			mris_convert --annot "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot "$FreeSurferFolder"/surf/"$hemisphere"h.white "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii
-			${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii $Structure
-			${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii -map 1 "$Subject"_"$Hemisphere"_"$Map"
-			${CARET7DIR}/wb_command -gifti-label-add-prefix "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii "${Hemisphere}_" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii
-		fi
-	done
-	#End main native mesh processing
-
-	#Copy Atlas Files
-	cp "$SurfaceAtlasDIR"/fs_"$Hemisphere"/fsaverage."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
-	cp "$SurfaceAtlasDIR"/fs_"$Hemisphere"/fs_"$Hemisphere"-to-fs_LR_fsaverage."$Hemisphere"_LR.spherical_std."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
-	cp "$SurfaceAtlasDIR"/fsaverage."$Hemisphere"_LR.spherical_std."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
-	${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
-	cp "$SurfaceAtlasDIR"/"$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii
-	cp "$SurfaceAtlasDIR"/"$Hemisphere".refsulc."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii
-	if [ -e "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii ] ; then
-		cp "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii
-	fi
-
-	#Concatenate FS registration to FS --> FS_LR registration
-	${CARET7DIR}/wb_command -surface-sphere-project-unproject "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.native.surf.gii "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii
-
-	#Make FreeSurfer Registration Areal Distortion Maps
-	${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii
-	${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
-	${CARET7DIR}/wb_command -metric-math "ln(spherereg / sphere) / ln(2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii -var sphere "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii -var spherereg "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
-	rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
-	${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_Areal_Distortion_FS
-	${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii MODE_AUTO_SCALE -palette-name ROY-BIG-BL -thresholding THRESHOLD_TYPE_NORMAL THRESHOLD_TEST_SHOW_OUTSIDE -1 1
-
-	${CARET7DIR}/wb_command -surface-distortion "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_FS.native.shape.gii -edge-method
-
-	${CARET7DIR}/wb_command -surface-distortion "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_FS.native.shape.gii -local-affine-method
-	${CARET7DIR}/wb_command -metric-merge "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_FS.native.shape.gii -metric "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_FS.native.shape.gii -column 1
-	${CARET7DIR}/wb_command -metric-merge "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_FS.native.shape.gii -metric "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_FS.native.shape.gii -column 2
-	${CARET7DIR}/wb_command -metric-math "ln(var) / ln (2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_FS.native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_FS.native.shape.gii
-	${CARET7DIR}/wb_command -metric-math "ln(var) / ln (2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_FS.native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_FS.native.shape.gii
-	rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_FS.native.shape.gii
-
-	#If desired, run MSMSulc folding-based registration to FS_LR initialized with FS affine
-	if [ ${RegName} = "MSMSulc" ] ; then
-		#Calculate Affine Transform and Apply
-		if [ ! -e "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc ] ; then
-			mkdir "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc
-		fi
-		${CARET7DIR}/wb_command -surface-affine-regression "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.mat
-		${CARET7DIR}/wb_command -surface-apply-affine "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.mat "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii
-		${CARET7DIR}/wb_command -surface-modify-sphere "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii 100 "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii
-		cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
-		DIR=$(pwd)
-		cd "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc
-		#Register using FreeSurfer Sulc Folding Map Using MSM Algorithm Configured for Reduced Distortion
-		#${MSMBINDIR}/msm --version
-		#${MSMBINDIR}/msm --levels=4 --conf=${MSMCONFIGDIR}/allparameterssulcDRconf --inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --trans="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii --indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii --refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose
-		${MSMBINDIR}/msm --conf=${MSMCONFIGDIR}/MSMSulcStrainFinalconf --inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii --indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii --refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose
-		cp ${MSMCONFIGDIR}/MSMSulcStrainFinalconf "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.logdir/conf
-		cd $DIR
-		#cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.HIGHRES_transformed.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii
-		cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere.reg.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii
-		${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii ${Structure}
-
-		#Make MSMSulc Registration Areal Distortion Maps
-		${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii
-		${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.shape.gii
-		${CARET7DIR}/wb_command -metric-math "ln(spherereg / sphere) / ln(2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii -var sphere "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii -var spherereg "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.shape.gii
-		rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.shape.gii
-		${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_Areal_Distortion_MSMSulc
-		${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii MODE_AUTO_SCALE -palette-name ROY-BIG-BL -thresholding THRESHOLD_TYPE_NORMAL THRESHOLD_TEST_SHOW_OUTSIDE -1 1
-
-		${CARET7DIR}/wb_command -surface-distortion "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.MSMSulc.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc.native.shape.gii -edge-method
-
-		${CARET7DIR}/wb_command -surface-distortion "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.MSMSulc.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii -local-affine-method
-		${CARET7DIR}/wb_command -metric-merge "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii -metric "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii -column 1
-		${CARET7DIR}/wb_command -metric-merge "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii -metric "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii -column 2
-		${CARET7DIR}/wb_command -metric-math "ln(var) / ln (2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii
-		${CARET7DIR}/wb_command -metric-math "ln(var) / ln (2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii
-		rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii
-
-		RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii"
-	else
-		RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii"
-	fi
-
-	#Ensure no zeros in atlas medial wall ROI
-	${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ${RegSphere} BARYCENTRIC "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".atlasroi.native.shape.gii -largest
-	${CARET7DIR}/wb_command -metric-math "(atlas + individual) > 0" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var atlas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".atlasroi.native.shape.gii -var individual "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-	${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
-	${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii
-
-
-	#Populate Highres fs_LR spec file.  Deform surfaces and other data according to native to folding-based registration selected above.  Regenerate inflated surfaces.
-	for Surface in white midthickness pial ; do
-		${CARET7DIR}/wb_command -surface-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Surface"."$HighResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Surface"."$HighResMesh"k_fs_LR.surf.gii
-	done
-
-	#HCP fsaverage_LR32k used -iterations-scale 0.75. Compute new param value for high res mesh density
-	HighResInflationScale=$(echo "scale=4; $InflateExtraScale * 0.75 * $HighResMesh / 32" | bc -l)
-
-	${CARET7DIR}/wb_command -surface-generate-inflated "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".inflated."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".very_inflated."$HighResMesh"k_fs_LR.surf.gii -iterations-scale $HighResInflationScale
-	${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".inflated."$HighResMesh"k_fs_LR.surf.gii
-	${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".very_inflated."$HighResMesh"k_fs_LR.surf.gii
-
-	for Map in thickness curvature ; do
-		${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii -current-roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-		${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii
-	done
-	${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
-	${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".EdgeDistortion_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
-	${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".StrainJ_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
-	${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".StrainR_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
-	if [ ${RegName} = "MSMSulc" ] ; then
-		${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
-	fi
-	${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
-
-	for Map in aparc aparc.a2009s ; do #Remove BA because it doesn't convert properly
-		if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
-			${CARET7DIR}/wb_command -label-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.label.gii -largest
-		fi
-	done
-
-	for LowResMesh in ${LowResMeshes} ; do
-		#Copy Atlas Files
-		cp "$SurfaceAtlasDIR"/"$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii
-		cp "$GrayordinatesSpaceDIR"/"$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii
-		if [ -e "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii ] ; then
-			cp "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii
-			${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii
-		fi
-
-		#Create downsampled fs_LR spec files.
-		for Surface in white midthickness pial ; do
-			${CARET7DIR}/wb_command -surface-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
-			${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
-		done
-
-		#HCP fsaverage_LR32k used -iterations-scale 0.75. Recalculate in case using a different mesh
-		LowResInflationScale=$(echo "scale=4; $InflateExtraScale * 0.75 * $LowResMesh / 32" | bc -l)
-
-		${CARET7DIR}/wb_command -surface-generate-inflated "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii -iterations-scale "$LowResInflationScale"
-		${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii
-
-		for Map in sulc thickness curvature ; do
-			${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii -current-roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
-			${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii
-		done
-		${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".ArealDistortion_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".EdgeDistortion_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".StrainJ_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".StrainR_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
-		if [ ${RegName} = "MSMSulc" ] ; then
-			${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
-			${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
-			${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".StrainJ_MSMSulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
-			${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".StrainR_MSMSulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
-		fi
-		${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
-
-		for Map in aparc aparc.a2009s ; do #Remove BA because it doesn't convert properly
-			if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
-				${CARET7DIR}/wb_command -label-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.label.gii -largest
-			fi
-		done
-
-		#Create downsampled fs_LR spec file in structural space.
-		for Surface in white midthickness pial ; do
-			${CARET7DIR}/wb_command -surface-resample "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
-			${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
-		done
-
-		#HCP fsaverage_LR32k used -iterations-scale 0.75. Recalculate in case using a different mesh
-		LowResInflationScale=$(echo "scale=4; $InflateExtraScale * 0.75 * $LowResMesh / 32" | bc -l)
-
-		${CARET7DIR}/wb_command -surface-generate-inflated "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii -iterations-scale "$LowResInflationScale"
-		${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii
-		${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii
-	done
+    #Set a bunch of different ways of saying left and right
+    if [ $Hemisphere = "L" ] ; then
+        hemisphere="l"
+        Structure="CORTEX_LEFT"
+    elif [ $Hemisphere = "R" ] ; then
+        hemisphere="r"
+        Structure="CORTEX_RIGHT"
+    fi
+
+    #native Mesh Processing
+    #Convert and volumetrically register white and pial surfaces makign linear and nonlinear copies, add each to the appropriate spec file
+    Types="ANATOMICAL@GRAY_WHITE ANATOMICAL@PIAL"
+    i=1
+    for Surface in white pial ; do
+        Type=$(echo "$Types" | cut -d " " -f $i)
+        Secondary=$(echo "$Type" | cut -d "@" -f 2)
+        Type=$(echo "$Type" | cut -d "@" -f 1)
+        if [ ! $Secondary = $Type ] ; then
+            Secondary=$(echo " -surface-secondary-type ""$Secondary")
+        else
+            Secondary=""
+        fi
+        mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$Surface" "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
+        ${CARET7DIR}/wb_command -set-structure "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type $Type$Secondary
+        ${CARET7DIR}/wb_command -surface-apply-affine "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii "$FreeSurferFolder"/mri/c_ras.mat "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
+        ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
+        ${CARET7DIR}/wb_command -surface-apply-warpfield "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii "$InverseAtlasTransform".nii.gz "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii -fnirt "$AtlasTransform".nii.gz
+        ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
+        i=$(( i+1 ))
+    done
+
+    #Create midthickness by averaging white and pial surfaces and use it to make inflated surfacess
+    for Folder in "$T1wFolder" "$AtlasSpaceFolder" ; do
+        ${CARET7DIR}/wb_command -surface-average "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii -surf "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".white.native.surf.gii -surf "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".pial.native.surf.gii
+        ${CARET7DIR}/wb_command -set-structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii ${Structure} -surface-type ANATOMICAL -surface-secondary-type MIDTHICKNESS
+        ${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii
+
+        #get number of vertices from native file
+        NativeVerts=$(${CARET7DIR}/wb_command -file-information "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii | grep 'Number of Vertices:' | cut -f2 -d: | tr -d '[:space:]')
+
+        #HCP fsaverage_LR32k used -iterations-scale 0.75. Compute new param value for native mesh density
+        NativeInflationScale=$(echo "scale=4; $InflateExtraScale * 0.75 * $NativeVerts / 32492" | bc -l)
+
+        ${CARET7DIR}/wb_command -surface-generate-inflated "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".inflated.native.surf.gii "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".very_inflated.native.surf.gii -iterations-scale $NativeInflationScale
+        ${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".inflated.native.surf.gii
+        ${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$Folder"/"$NativeFolder"/"$Subject"."$Hemisphere".very_inflated.native.surf.gii
+    done
+
+    #Convert original and registered spherical surfaces and add them to the nonlinear spec file
+    for Surface in sphere.reg sphere ; do
+        mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$Surface" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
+        ${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type SPHERICAL
+    done
+    ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii
+
+    #Add more files to the spec file and convert other FreeSurfer surface data to metric/GIFTI including sulc, curv, and thickness.
+    for Map in sulc@sulc@Sulc thickness@thickness@Thickness curv@curvature@Curvature ; do
+        fsname=$(echo $Map | cut -d "@" -f 1)
+        wbname=$(echo $Map | cut -d "@" -f 2)
+        mapname=$(echo $Map | cut -d "@" -f 3)
+        mris_convert -c "$FreeSurferFolder"/surf/"$hemisphere"h."$fsname" "$FreeSurferFolder"/surf/"$hemisphere"h.white "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii
+        ${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii ${Structure}
+        ${CARET7DIR}/wb_command -metric-math "var * -1" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii
+        ${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii -map 1 "$Subject"_"$Hemisphere"_"$mapname"
+        ${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii MODE_AUTO_SCALE_PERCENTAGE -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
+    done
+    #Thickness specific operations
+    ${CARET7DIR}/wb_command -metric-math "abs(thickness)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii -var thickness "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
+    ${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii MODE_AUTO_SCALE_PERCENTAGE -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
+    ${CARET7DIR}/wb_command -metric-math "thickness > 0" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var thickness "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
+    ${CARET7DIR}/wb_command -metric-fill-holes "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+    ${CARET7DIR}/wb_command -metric-remove-islands "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+    ${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_ROI
+    ${CARET7DIR}/wb_command -metric-dilate "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 10 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii -nearest
+    ${CARET7DIR}/wb_command -metric-dilate "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 10 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii -nearest
+
+    #Label operations
+    for Map in aparc aparc.a2009s ; do #Remove BA because it doesn't convert properly
+        if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
+            mris_convert --annot "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot "$FreeSurferFolder"/surf/"$hemisphere"h.white "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii
+            ${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii $Structure
+            ${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii -map 1 "$Subject"_"$Hemisphere"_"$Map"
+            ${CARET7DIR}/wb_command -gifti-label-add-prefix "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii "${Hemisphere}_" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii
+        fi
+    done
+    #End main native mesh processing
+
+    #Copy Atlas Files
+    cp "$SurfaceAtlasDIR"/fs_"$Hemisphere"/fsaverage."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
+    cp "$SurfaceAtlasDIR"/fs_"$Hemisphere"/fs_"$Hemisphere"-to-fs_LR_fsaverage."$Hemisphere"_LR.spherical_std."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
+    cp "$SurfaceAtlasDIR"/fsaverage."$Hemisphere"_LR.spherical_std."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
+    ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
+    cp "$SurfaceAtlasDIR"/"$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii
+    cp "$SurfaceAtlasDIR"/"$Hemisphere".refsulc."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii
+    if [ -e "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii ] ; then
+        cp "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii
+    fi
+
+    #Concatenate FS registration to FS --> FS_LR registration
+    ${CARET7DIR}/wb_command -surface-sphere-project-unproject "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.native.surf.gii "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii
+
+    #Make FreeSurfer Registration Areal Distortion Maps
+    ${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii
+    ${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
+    ${CARET7DIR}/wb_command -metric-math "ln(spherereg / sphere) / ln(2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii -var sphere "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii -var spherereg "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
+    rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
+    ${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_Areal_Distortion_FS
+    ${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii MODE_AUTO_SCALE -palette-name ROY-BIG-BL -thresholding THRESHOLD_TYPE_NORMAL THRESHOLD_TEST_SHOW_OUTSIDE -1 1
+
+    ${CARET7DIR}/wb_command -surface-distortion "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_FS.native.shape.gii -edge-method
+
+    ${CARET7DIR}/wb_command -surface-distortion "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_FS.native.shape.gii -local-affine-method
+    ${CARET7DIR}/wb_command -metric-merge "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_FS.native.shape.gii -metric "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_FS.native.shape.gii -column 1
+    ${CARET7DIR}/wb_command -metric-merge "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_FS.native.shape.gii -metric "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_FS.native.shape.gii -column 2
+    ${CARET7DIR}/wb_command -metric-math "ln(var) / ln (2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_FS.native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_FS.native.shape.gii
+    ${CARET7DIR}/wb_command -metric-math "ln(var) / ln (2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_FS.native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_FS.native.shape.gii
+    rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_FS.native.shape.gii
+
+    #If desired, run MSMSulc folding-based registration to FS_LR initialized with FS affine
+    if [ ${RegName} = "MSMSulc" ] ; then
+        #Calculate Affine Transform and Apply
+        if [ ! -e "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc ] ; then
+            mkdir "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc
+        fi
+        ${CARET7DIR}/wb_command -surface-affine-regression "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.mat
+        ${CARET7DIR}/wb_command -surface-apply-affine "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.mat "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii
+        ${CARET7DIR}/wb_command -surface-modify-sphere "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii 100 "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii
+        cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere_rot.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
+        DIR=$(pwd)
+        cd "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc
+        #Register using FreeSurfer Sulc Folding Map Using MSM Algorithm Configured for Reduced Distortion
+        #${MSMBINDIR}/msm --version
+        #${MSMBINDIR}/msm --levels=4 --conf=${MSMCONFIGDIR}/allparameterssulcDRconf --inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --trans="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii --indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii --refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose
+        ${MSMBINDIR}/msm --conf=${MSMCONFIGDIR}/MSMSulcStrainFinalconf --inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii --indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii --refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose
+        cp ${MSMCONFIGDIR}/MSMSulcStrainFinalconf "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.logdir/conf
+        cd $DIR
+        #cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.HIGHRES_transformed.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii
+        cp "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.sphere.reg.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii
+        ${CARET7DIR}/wb_command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii ${Structure}
+
+        #Make MSMSulc Registration Areal Distortion Maps
+        ${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii
+        ${CARET7DIR}/wb_command -surface-vertex-areas "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.shape.gii
+        ${CARET7DIR}/wb_command -metric-math "ln(spherereg / sphere) / ln(2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii -var sphere "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii -var spherereg "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.shape.gii
+        rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.shape.gii
+        ${CARET7DIR}/wb_command -set-map-names "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_Areal_Distortion_MSMSulc
+        ${CARET7DIR}/wb_command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii MODE_AUTO_SCALE -palette-name ROY-BIG-BL -thresholding THRESHOLD_TYPE_NORMAL THRESHOLD_TEST_SHOW_OUTSIDE -1 1
+
+        ${CARET7DIR}/wb_command -surface-distortion "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.MSMSulc.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc.native.shape.gii -edge-method
+
+        ${CARET7DIR}/wb_command -surface-distortion "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.MSMSulc.native.surf.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii -local-affine-method
+        ${CARET7DIR}/wb_command -metric-merge "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii -metric "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii -column 1
+        ${CARET7DIR}/wb_command -metric-merge "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii -metric "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii -column 2
+        ${CARET7DIR}/wb_command -metric-math "ln(var) / ln (2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii
+        ${CARET7DIR}/wb_command -metric-math "ln(var) / ln (2)" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii -var var "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii
+        rm "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".Strain_MSMSulc.native.shape.gii
+
+        RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii"
+    else
+        RegSphere="${AtlasSpaceFolder}/${NativeFolder}/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii"
+    fi
+
+    #Ensure no zeros in atlas medial wall ROI
+    ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ${RegSphere} BARYCENTRIC "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".atlasroi.native.shape.gii -largest
+    ${CARET7DIR}/wb_command -metric-math "(atlas + individual) > 0" "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var atlas "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".atlasroi.native.shape.gii -var individual "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+    ${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
+    ${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii
+
+
+    #Populate Highres fs_LR spec file.  Deform surfaces and other data according to native to folding-based registration selected above.  Regenerate inflated surfaces.
+    for Surface in white midthickness pial ; do
+        ${CARET7DIR}/wb_command -surface-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Surface"."$HighResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Surface"."$HighResMesh"k_fs_LR.surf.gii
+    done
+
+    #HCP fsaverage_LR32k used -iterations-scale 0.75. Compute new param value for high res mesh density
+    HighResInflationScale=$(echo "scale=4; $InflateExtraScale * 0.75 * $HighResMesh / 32" | bc -l)
+
+    ${CARET7DIR}/wb_command -surface-generate-inflated "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".inflated."$HighResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".very_inflated."$HighResMesh"k_fs_LR.surf.gii -iterations-scale $HighResInflationScale
+    ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".inflated."$HighResMesh"k_fs_LR.surf.gii
+    ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".very_inflated."$HighResMesh"k_fs_LR.surf.gii
+
+    for Map in thickness curvature ; do
+        ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii -current-roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+        ${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii
+    done
+    ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
+    ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".EdgeDistortion_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
+    ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".StrainJ_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
+    ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".StrainR_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
+    if [ ${RegName} = "MSMSulc" ] ; then
+        ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
+    fi
+    ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
+
+    for Map in aparc aparc.a2009s ; do #Remove BA because it doesn't convert properly
+        if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
+            ${CARET7DIR}/wb_command -label-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii ${RegSphere} "$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.label.gii -largest
+        fi
+    done
+
+    for LowResMesh in ${LowResMeshes} ; do
+        #Copy Atlas Files
+        cp "$SurfaceAtlasDIR"/"$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii
+        cp "$GrayordinatesSpaceDIR"/"$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii
+        if [ -e "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii ] ; then
+            cp "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii
+            ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii
+        fi
+
+        #Create downsampled fs_LR spec files.
+        for Surface in white midthickness pial ; do
+            ${CARET7DIR}/wb_command -surface-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
+            ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
+        done
+
+        #HCP fsaverage_LR32k used -iterations-scale 0.75. Recalculate in case using a different mesh
+        LowResInflationScale=$(echo "scale=4; $InflateExtraScale * 0.75 * $LowResMesh / 32" | bc -l)
+
+        ${CARET7DIR}/wb_command -surface-generate-inflated "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii -iterations-scale "$LowResInflationScale"
+        ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii
+
+        for Map in sulc thickness curvature ; do
+            ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii -current-roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
+            ${CARET7DIR}/wb_command -metric-mask "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii
+        done
+        ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".ArealDistortion_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".EdgeDistortion_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".StrainJ_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_FS.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".StrainR_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
+        if [ ${RegName} = "MSMSulc" ] ; then
+            ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".ArealDistortion_MSMSulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
+            ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".EdgeDistortion_MSMSulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
+            ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainJ_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".StrainJ_MSMSulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
+            ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".StrainR_MSMSulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".StrainR_MSMSulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
+        fi
+        ${CARET7DIR}/wb_command -metric-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
+
+        for Map in aparc aparc.a2009s ; do #Remove BA because it doesn't convert properly
+            if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
+                ${CARET7DIR}/wb_command -label-resample "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.label.gii -largest
+            fi
+        done
+
+        #Create downsampled fs_LR spec file in structural space.
+        for Surface in white midthickness pial ; do
+            ${CARET7DIR}/wb_command -surface-resample "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
+            ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
+        done
+
+        #HCP fsaverage_LR32k used -iterations-scale 0.75. Recalculate in case using a different mesh
+        LowResInflationScale=$(echo "scale=4; $InflateExtraScale * 0.75 * $LowResMesh / 32" | bc -l)
+
+        ${CARET7DIR}/wb_command -surface-generate-inflated "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii -iterations-scale "$LowResInflationScale"
+        ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii
+        ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii
+    done
 done
 
 STRINGII=""
 for LowResMesh in ${LowResMeshes} ; do
-	STRINGII=$(echo "${STRINGII}${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR@atlasroi ")
+    STRINGII=$(echo "${STRINGII}${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR@atlasroi ")
 done
 
 #Create CIFTI Files
 for STRING in "$AtlasSpaceFolder"/"$NativeFolder"@native@roi "$AtlasSpaceFolder"@"$HighResMesh"k_fs_LR@atlasroi ${STRINGII} ; do
-	Folder=$(echo $STRING | cut -d "@" -f 1)
-	Mesh=$(echo $STRING | cut -d "@" -f 2)
-	ROI=$(echo $STRING | cut -d "@" -f 3)
-
-	${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.sulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.sulc."$Mesh".shape.gii
-	${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -map 1 "${Subject}_Sulc"
-	${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
-
-	${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.curvature."$Mesh".shape.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.curvature."$Mesh".shape.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
-	${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -map 1 "${Subject}_Curvature"
-	${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
-
-	${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.thickness."$Mesh".shape.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.thickness."$Mesh".shape.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
-	${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -map 1 "${Subject}_Thickness"
-	${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
-
-	${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.ArealDistortion_FS."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.ArealDistortion_FS."$Mesh".shape.gii
-	${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -map 1 "${Subject}_ArealDistortion_FS"
-	${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
-
-	${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".EdgeDistortion_FS."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.EdgeDistortion_FS."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.EdgeDistortion_FS."$Mesh".shape.gii
-	${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".EdgeDistortion_FS."$Mesh".dscalar.nii -map 1 "${Subject}_EdgeDistortion_FS"
-	${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".EdgeDistortion_FS."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".EdgeDistortion_FS."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
-
-	${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".StrainJ_FS."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.StrainJ_FS."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.StrainJ_FS."$Mesh".shape.gii
-	${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".StrainJ_FS."$Mesh".dscalar.nii -map 1 "${Subject}_StrainJ_FS"
-	${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".StrainJ_FS."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".StrainJ_FS."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
-
-	${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".StrainR_FS."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.StrainR_FS."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.StrainR_FS."$Mesh".shape.gii
-	${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".StrainR_FS."$Mesh".dscalar.nii -map 1 "${Subject}_StrainR_FS"
-	${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".StrainR_FS."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".StrainR_FS."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
-
-	if [ ${RegName} = "MSMSulc" ] ; then
-		${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.ArealDistortion_MSMSulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.ArealDistortion_MSMSulc."$Mesh".shape.gii
-		${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii -map 1 "${Subject}_ArealDistortion_MSMSulc"
-		${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
-
-		${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".EdgeDistortion_MSMSulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.EdgeDistortion_MSMSulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.EdgeDistortion_MSMSulc."$Mesh".shape.gii
-		${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".EdgeDistortion_MSMSulc."$Mesh".dscalar.nii -map 1 "${Subject}_EdgeDistortion_MSMSulc"
-		${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".EdgeDistortion_MSMSulc."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".EdgeDistortion_MSMSulc."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
-
-		${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".StrainJ_MSMSulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.StrainJ_MSMSulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.StrainJ_MSMSulc."$Mesh".shape.gii
-		${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".StrainJ_MSMSulc."$Mesh".dscalar.nii -map 1 "${Subject}_StrainJ_MSMSulc"
-		${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".StrainJ_MSMSulc."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".StrainJ_MSMSulc."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
-
-		${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".StrainR_MSMSulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.StrainR_MSMSulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.StrainR_MSMSulc."$Mesh".shape.gii
-		${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".StrainR_MSMSulc."$Mesh".dscalar.nii -map 1 "${Subject}_StrainR_MSMSulc"
-		${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".StrainR_MSMSulc."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".StrainR_MSMSulc."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
-	fi
-
-	for Map in aparc aparc.a2009s ; do #Remove BA because it doesn't convert properly
-		if [ -e "$Folder"/"$Subject".L.${Map}."$Mesh".label.gii ] ; then
-			${CARET7DIR}/wb_command -cifti-create-label "$Folder"/"$Subject".${Map}."$Mesh".dlabel.nii -left-label "$Folder"/"$Subject".L.${Map}."$Mesh".label.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-label "$Folder"/"$Subject".R.${Map}."$Mesh".label.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
-			${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".${Map}."$Mesh".dlabel.nii -map 1 "$Subject"_${Map}
-		fi
-	done
+    Folder=$(echo $STRING | cut -d "@" -f 1)
+    Mesh=$(echo $STRING | cut -d "@" -f 2)
+    ROI=$(echo $STRING | cut -d "@" -f 3)
+
+    ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.sulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.sulc."$Mesh".shape.gii
+    ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -map 1 "${Subject}_Sulc"
+    ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
+
+    ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.curvature."$Mesh".shape.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.curvature."$Mesh".shape.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
+    ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -map 1 "${Subject}_Curvature"
+    ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
+
+    ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.thickness."$Mesh".shape.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.thickness."$Mesh".shape.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
+    ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -map 1 "${Subject}_Thickness"
+    ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
+
+    ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.ArealDistortion_FS."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.ArealDistortion_FS."$Mesh".shape.gii
+    ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -map 1 "${Subject}_ArealDistortion_FS"
+    ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
+
+    ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".EdgeDistortion_FS."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.EdgeDistortion_FS."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.EdgeDistortion_FS."$Mesh".shape.gii
+    ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".EdgeDistortion_FS."$Mesh".dscalar.nii -map 1 "${Subject}_EdgeDistortion_FS"
+    ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".EdgeDistortion_FS."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".EdgeDistortion_FS."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
+
+    ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".StrainJ_FS."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.StrainJ_FS."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.StrainJ_FS."$Mesh".shape.gii
+    ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".StrainJ_FS."$Mesh".dscalar.nii -map 1 "${Subject}_StrainJ_FS"
+    ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".StrainJ_FS."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".StrainJ_FS."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
+
+    ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".StrainR_FS."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.StrainR_FS."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.StrainR_FS."$Mesh".shape.gii
+    ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".StrainR_FS."$Mesh".dscalar.nii -map 1 "${Subject}_StrainR_FS"
+    ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".StrainR_FS."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".StrainR_FS."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
+
+    if [ ${RegName} = "MSMSulc" ] ; then
+        ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.ArealDistortion_MSMSulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.ArealDistortion_MSMSulc."$Mesh".shape.gii
+        ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii -map 1 "${Subject}_ArealDistortion_MSMSulc"
+        ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".ArealDistortion_MSMSulc."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
+
+        ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".EdgeDistortion_MSMSulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.EdgeDistortion_MSMSulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.EdgeDistortion_MSMSulc."$Mesh".shape.gii
+        ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".EdgeDistortion_MSMSulc."$Mesh".dscalar.nii -map 1 "${Subject}_EdgeDistortion_MSMSulc"
+        ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".EdgeDistortion_MSMSulc."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".EdgeDistortion_MSMSulc."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
+
+        ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".StrainJ_MSMSulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.StrainJ_MSMSulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.StrainJ_MSMSulc."$Mesh".shape.gii
+        ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".StrainJ_MSMSulc."$Mesh".dscalar.nii -map 1 "${Subject}_StrainJ_MSMSulc"
+        ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".StrainJ_MSMSulc."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".StrainJ_MSMSulc."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
+
+        ${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".StrainR_MSMSulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.StrainR_MSMSulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.StrainR_MSMSulc."$Mesh".shape.gii
+        ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".StrainR_MSMSulc."$Mesh".dscalar.nii -map 1 "${Subject}_StrainR_MSMSulc"
+        ${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".StrainR_MSMSulc."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".StrainR_MSMSulc."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
+    fi
+
+    for Map in aparc aparc.a2009s ; do #Remove BA because it doesn't convert properly
+        if [ -e "$Folder"/"$Subject".L.${Map}."$Mesh".label.gii ] ; then
+            ${CARET7DIR}/wb_command -cifti-create-label "$Folder"/"$Subject".${Map}."$Mesh".dlabel.nii -left-label "$Folder"/"$Subject".L.${Map}."$Mesh".label.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-label "$Folder"/"$Subject".R.${Map}."$Mesh".label.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
+            ${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".${Map}."$Mesh".dlabel.nii -map 1 "$Subject"_${Map}
+        fi
+    done
 done
 
 STRINGII=""
 for LowResMesh in ${LowResMeshes} ; do
-	STRINGII=$(echo "${STRINGII}${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR ${T1wFolder}/fsaverage_LR${LowResMesh}k@${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR ")
+    STRINGII=$(echo "${STRINGII}${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR ${T1wFolder}/fsaverage_LR${LowResMesh}k@${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR ")
 done
 
 #Add CIFTI Maps to Spec Files
 for STRING in "$T1wFolder"/"$NativeFolder"@"$AtlasSpaceFolder"/"$NativeFolder"@native "$AtlasSpaceFolder"/"$NativeFolder"@"$AtlasSpaceFolder"/"$NativeFolder"@native "$AtlasSpaceFolder"@"$AtlasSpaceFolder"@"$HighResMesh"k_fs_LR ${STRINGII} ; do
-	FolderI=$(echo $STRING | cut -d "@" -f 1)
-	FolderII=$(echo $STRING | cut -d "@" -f 2)
-	Mesh=$(echo $STRING | cut -d "@" -f 3)
-	for STRINGII in sulc@dscalar thickness@dscalar curvature@dscalar aparc@dlabel aparc.a2009s@dlabel ; do #Remove BA@dlabel because it doesn't convert properly
-		Map=$(echo $STRINGII | cut -d "@" -f 1)
-		Ext=$(echo $STRINGII | cut -d "@" -f 2)
-		if [ -e "$FolderII"/"$Subject"."$Map"."$Mesh"."$Ext".nii ] ; then
-			${CARET7DIR}/wb_command -add-to-spec-file "$FolderI"/"$Subject"."$Mesh".wb.spec INVALID "$FolderII"/"$Subject"."$Map"."$Mesh"."$Ext".nii
-		fi
-	done
+    FolderI=$(echo $STRING | cut -d "@" -f 1)
+    FolderII=$(echo $STRING | cut -d "@" -f 2)
+    Mesh=$(echo $STRING | cut -d "@" -f 3)
+    for STRINGII in sulc@dscalar thickness@dscalar curvature@dscalar aparc@dlabel aparc.a2009s@dlabel ; do #Remove BA@dlabel because it doesn't convert properly
+        Map=$(echo $STRINGII | cut -d "@" -f 1)
+        Ext=$(echo $STRINGII | cut -d "@" -f 2)
+        if [ -e "$FolderII"/"$Subject"."$Map"."$Mesh"."$Ext".nii ] ; then
+            ${CARET7DIR}/wb_command -add-to-spec-file "$FolderI"/"$Subject"."$Mesh".wb.spec INVALID "$FolderII"/"$Subject"."$Map"."$Mesh"."$Ext".nii
+        fi
+    done
 done
 
 # Create midthickness Vertex Area (VA) maps
@@ -559,48 +562,48 @@ log_Msg "Create midthickness Vertex Area (VA) maps"
 
 for LowResMesh in ${LowResMeshes} ; do
 
-	log_Msg "Creating midthickness Vertex Area (VA) maps for LowResMesh: ${LowResMesh}"
+    log_Msg "Creating midthickness Vertex Area (VA) maps for LowResMesh: ${LowResMesh}"
 
-	# DownSampleT1wFolder             - path to folder containing downsampled T1w files
-	# midthickness_va_file            - path to non-normalized midthickness vertex area file
-	# normalized_midthickness_va_file - path ot normalized midthickness vertex area file
-	# surface_to_measure              - path to surface file on which to measure surface areas
-	# output_metric                   - path to metric file generated by -surface-vertex-areas subcommand
+    # DownSampleT1wFolder             - path to folder containing downsampled T1w files
+    # midthickness_va_file            - path to non-normalized midthickness vertex area file
+    # normalized_midthickness_va_file - path ot normalized midthickness vertex area file
+    # surface_to_measure              - path to surface file on which to measure surface areas
+    # output_metric                   - path to metric file generated by -surface-vertex-areas subcommand
 
-	DownSampleT1wFolder=${T1wFolder}/fsaverage_LR${LowResMesh}k
-	DownSampleFolder=${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k
-	midthickness_va_file=${DownSampleT1wFolder}/${Subject}.midthickness_va.${LowResMesh}k_fs_LR.dscalar.nii
-	normalized_midthickness_va_file=${DownSampleT1wFolder}/${Subject}.midthickness_va_norm.${LowResMesh}k_fs_LR.dscalar.nii
+    DownSampleT1wFolder=${T1wFolder}/fsaverage_LR${LowResMesh}k
+    DownSampleFolder=${AtlasSpaceFolder}/fsaverage_LR${LowResMesh}k
+    midthickness_va_file=${DownSampleT1wFolder}/${Subject}.midthickness_va.${LowResMesh}k_fs_LR.dscalar.nii
+    normalized_midthickness_va_file=${DownSampleT1wFolder}/${Subject}.midthickness_va_norm.${LowResMesh}k_fs_LR.dscalar.nii
 
-	for Hemisphere in L R ; do
-		surface_to_measure=${DownSampleT1wFolder}/${Subject}.${Hemisphere}.midthickness.${LowResMesh}k_fs_LR.surf.gii
-		output_metric=${DownSampleT1wFolder}/${Subject}.${Hemisphere}.midthickness_va.${LowResMesh}k_fs_LR.shape.gii
-		${CARET7DIR}/wb_command -surface-vertex-areas ${surface_to_measure} ${output_metric}
-	done
+    for Hemisphere in L R ; do
+        surface_to_measure=${DownSampleT1wFolder}/${Subject}.${Hemisphere}.midthickness.${LowResMesh}k_fs_LR.surf.gii
+        output_metric=${DownSampleT1wFolder}/${Subject}.${Hemisphere}.midthickness_va.${LowResMesh}k_fs_LR.shape.gii
+        ${CARET7DIR}/wb_command -surface-vertex-areas ${surface_to_measure} ${output_metric}
+    done
 
-	# left_metric  - path to left hemisphere VA metric file
-	# roi_left     - path to file of ROI vertices to use from left surface
-	# right_metric - path to right hemisphere VA metric file
-	# roi_right    - path to file of ROI vertices to use from right surface
+    # left_metric  - path to left hemisphere VA metric file
+    # roi_left     - path to file of ROI vertices to use from left surface
+    # right_metric - path to right hemisphere VA metric file
+    # roi_right    - path to file of ROI vertices to use from right surface
 
-	left_metric=${DownSampleT1wFolder}/${Subject}.L.midthickness_va.${LowResMesh}k_fs_LR.shape.gii
-	roi_left=${DownSampleFolder}/${Subject}.L.atlasroi.${LowResMesh}k_fs_LR.shape.gii
-	right_metric=${DownSampleT1wFolder}/${Subject}.R.midthickness_va.${LowResMesh}k_fs_LR.shape.gii
-	roi_right=${DownSampleFolder}/${Subject}.R.atlasroi.${LowResMesh}k_fs_LR.shape.gii
+    left_metric=${DownSampleT1wFolder}/${Subject}.L.midthickness_va.${LowResMesh}k_fs_LR.shape.gii
+    roi_left=${DownSampleFolder}/${Subject}.L.atlasroi.${LowResMesh}k_fs_LR.shape.gii
+    right_metric=${DownSampleT1wFolder}/${Subject}.R.midthickness_va.${LowResMesh}k_fs_LR.shape.gii
+    roi_right=${DownSampleFolder}/${Subject}.R.atlasroi.${LowResMesh}k_fs_LR.shape.gii
 
-	${CARET7DIR}/wb_command -cifti-create-dense-scalar ${midthickness_va_file} \
-				-left-metric  ${left_metric} \
-				-roi-left     ${roi_left} \
-				-right-metric ${right_metric} \
-				-roi-right    ${roi_right}
+    ${CARET7DIR}/wb_command -cifti-create-dense-scalar ${midthickness_va_file} \
+                -left-metric  ${left_metric} \
+                -roi-left     ${roi_left} \
+                -right-metric ${right_metric} \
+                -roi-right    ${roi_right}
 
-	# VAMean - mean of surface area accounted for for each vertex - used for normalization
-	VAMean=$(${CARET7DIR}/wb_command -cifti-stats ${midthickness_va_file} -reduce MEAN)
-	log_Msg "VAMean: ${VAMean}"
+    # VAMean - mean of surface area accounted for for each vertex - used for normalization
+    VAMean=$(${CARET7DIR}/wb_command -cifti-stats ${midthickness_va_file} -reduce MEAN)
+    log_Msg "VAMean: ${VAMean}"
 
-	${CARET7DIR}/wb_command -cifti-math "VA / ${VAMean}" ${normalized_midthickness_va_file} -var VA ${midthickness_va_file}
+    ${CARET7DIR}/wb_command -cifti-math "VA / ${VAMean}" ${normalized_midthickness_va_file} -var VA ${midthickness_va_file}
 
-	log_Msg "Done creating midthickness Vertex Area (VA) maps for LowResMesh: ${LowResMesh}"
+    log_Msg "Done creating midthickness Vertex Area (VA) maps for LowResMesh: ${LowResMesh}"
 
 done
 
diff --git a/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear_1res.sh b/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear_1res.sh
index 3d2d3d4d7..0bf255ea7 100755
--- a/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear_1res.sh
+++ b/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear_1res.sh
@@ -6,10 +6,10 @@ set -e
 # ------------------------------------------------------------------------------
 
 if [ -z "${HCPPIPEDIR}" ]; then
-	echo "$(basename ${0}): ABORTING: HCPPIPEDIR environment variable must be set"
-	exit 1
+  echo "$(basename ${0}): ABORTING: HCPPIPEDIR environment variable must be set"
+  exit 1
 else
-	echo "$(basename ${0}): HCPPIPEDIR: ${HCPPIPEDIR}"
+  echo "$(basename ${0}): HCPPIPEDIR: ${HCPPIPEDIR}"
 fi
 
 # ------------------------------------------------------------------------------
@@ -28,21 +28,21 @@ log_Err_Abort "Script needs to be adapted to support use of strain-based MSM"
 # ------------------------------------------------------------------------------
 
 if [ -z "${MSMBINDIR}" ]; then
-	log_Err_Abort "MSMBINDIR environment variable must be set"
+  log_Err_Abort "MSMBINDIR environment variable must be set"
 else
-	log_Msg "MSMBINDIR: ${MSMBINDIR}"
+  log_Msg "MSMBINDIR: ${MSMBINDIR}"
 fi
 
 if [ -z "${MSMCONFIGDIR}" ]; then
-	log_Err_Abort "MSMCONFIGDIR environment variable must be set"
+  log_Err_Abort "MSMCONFIGDIR environment variable must be set"
 else
-	log_Msg "MSMCONFIGDIR: ${MSMCONFIGDIR}"
+  log_Msg "MSMCONFIGDIR: ${MSMCONFIGDIR}"
 fi
 
 if [ -z "${CARET7DIR}" ]; then
-	log_Err_Abort "CARET7DIR environment variable must be set"
+  log_Err_Abort "CARET7DIR environment variable must be set"
 else
-	log_Msg "CARET7DIR: ${CARET7DIR}"
+  log_Msg "CARET7DIR: ${CARET7DIR}"
 fi
 
 
@@ -104,10 +104,10 @@ done
 
 
 for LowResMesh in ${LowResMeshes} ; do
-  ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
+  [ "${T2wImage}" != "NONE" ] && ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz
   ${CARET7DIR}/wb_command -add-to-spec-file "$AtlasSpaceFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage".nii.gz
 
-  ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$T1wFolder"/"$T2wImage".nii.gz
+  [ "${T2wImage}" != "NONE" ] && ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$T1wFolder"/"$T2wImage".nii.gz
   ${CARET7DIR}/wb_command -add-to-spec-file "$T1wFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID "$T1wFolder"/"$T1wImage".nii.gz
 done
 
@@ -119,7 +119,7 @@ for GrayordinatesResolution in ${GrayordinatesResolutions} ; do
   applywarp --interp=nn -i "$SurfaceAtlasDIR"/Avgwmparc.nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz
   ${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz "$FreeSurferLabels" "$AtlasSpaceFolder"/ROIs/Atlas_wmparc."$GrayordinatesResolution".nii.gz -drop-unused-labels
   ${CARET7DIR}/wb_command -volume-label-import "$AtlasSpaceFolder"/ROIs/wmparc."$GrayordinatesResolution".nii.gz ${SubcorticalGrayLabels} "$AtlasSpaceFolder"/ROIs/ROIs."$GrayordinatesResolution".nii.gz -discard-others
-  applywarp --interp=spline -i "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage"."$GrayordinatesResolution".nii.gz
+  [ "${T2wImage}" != "NONE" ] && applywarp --interp=spline -i "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$AtlasSpaceT2wImage"."$GrayordinatesResolution".nii.gz
   applywarp --interp=spline -i "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage".nii.gz -r "$AtlasSpaceFolder"/ROIs/Atlas_ROIs."$GrayordinatesResolution".nii.gz -o "$AtlasSpaceFolder"/"$AtlasSpaceT1wImage"."$GrayordinatesResolution".nii.gz
 done