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, "hcp-users-boun...@humanconnectome.org on behalf of C.D. Langen" <hcp-users-boun...@humanconnectome.org on behalf of c.lan...@erasmusmc.nl> 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 > >_______________________________________________ >HCP-Users mailing list >HCP-Users@humanconnectome.org >http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users