those look like hcp commands so you should contact them
On 7/28/2022 2:00 PM, Ariana Fei wrote:
External Email - Use Caution
I'm attaching a list of command I used to convert freesurfer cortical
thickness output to native space:
$Caret5_Command -file-convert -fsc2c
"$FreeSurferFolder"/surf/"$hemisphere"h.thickness
"$FreeSurferFolder"/surf/"$hemisphere"h.white
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret5_Command -spec-file-add
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".native.c5.spec
surface_shape_file
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret5_Command -metric-set-column-name
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
1 "$Subject"_"$Hemisphere"_Thickness
$Caret5_Command -file-convert -format-convert XML_BASE64
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret7_Command -set-structure
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Structure
$Caret7_Command -add-to-spec-file
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec
$Structure
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret7_Command -metric-palette
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
MODE_AUTO_SCALE_PERCENTAGE -pos-percent 2 98 -palette-name Gray_Interp
-disp-pos true -disp-neg true -disp-zero true
#cp
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
"$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
#commented out GW
$Caret7_Command -add-to-spec-file
"$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure
"$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
This already gives negative cortical thickness values in native space.
Ariana
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