This is because FreeSurfer uses a more complicated coordinate system than
Connectome Workbench. The next version of FreeSurfer will have some
options in mris_convert to fix this, but for now you can do the following:
#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
${CARET7DIR}/wb_command -surface-apply-affine
"$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.sur
f.gii "$FreeSurferFolder"/mri/c_ras.mat
"$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Surface".native.sur
f.gii
Peace,
Matt.
On 10/13/15, 9:32 AM, "[email protected] on behalf of
C.D. Langen" <[email protected] on behalf of
[email protected]> wrote:
>Greetings,
>
>I am trying to use wb_view to view freesurfer surfaces and to load an
>overlay from a freesurfer volume (in this case, wmparc), but when I load
>them both, they are not aligned (image attached). What can I do to get
>the surface and volumes into the same space?
>
>Here are the steps I have completed to get the surface and metric files:
>
>1. Convert pial surface to gifti: mris_convert lh.pial lh.pial.surf.gii
>2. Convert wmparc from mgz to nii: mri_convert wmparc.mgz
>wmparc_origSpace.nii.gz
>3. Map wmparc to pial surface: wb_command -volume-to-surface-mapping
>wmparc.nii.gz lh.pial.surf.gii wmparc.lh.shape.gii -trilinear
>
>Regards,
>Carolyn
>
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