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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.