I tried, here is the command: mris_make_surfaces -cover_seg mri/aseg.mgz subjid lh
and the last 5 lines of the run: ... smoothing surface for 5 iterations... repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 creating distance transform volume from segmentation ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2 height=1. If this is it and not working, I wonder that editing the aseg to exclude the nonlesional GM outside the pia, but leaving/ adding lesional GM of interest, either under the GM label or a custom label would allow create a 'proper' volume, followed by surface generation. I known this is doable, the question is whether the generated surface can be registered to sphere and whether DK atlas can be applied (this is a more general question, whether any surface generated outside the default recon-all pathway can be registered to sphere and in effect become "pia" or another classical boundary surface?) example after labeling the lesion as 'o' (other): % generate mask from aseg cd /usr/local/fs5.3/freesurfer/subjects/subjid mris_fill -c -r 0.1 surf/rh.pial mri/rh.pial.filled.mgz && \ mris_fill -c -r 0.1 surf/lh.pial mri/lh.pial.filled.mgz && \ mri_concat --combine --i mri/rh.pial.filled.mgz --i mri/lh.pial.filled.mgz --o mri/pial.filled.mgz && \ cd ./mri && \ mri_binarize --i aseg.mgz --match o --o lesion.mask.mgz && \ fscalc pial.filled.mgz add lesion.mask.mgz -o pialmask.mgz && \ mri_convert brain.mgz brain.float.mgz -odt float && \ mri_mask brain.float.mgz pialmask.mgz pialbrain.mgz % generate new 'pial' surface: mri_tessellate mri/pialbrain.mgz -a surf/lh.pialbrain.pial Please advise, Octavian
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