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Hello all,

To create surfaces for a sheep brain using Freesurfer version 5.3 I previously used, mris_make_surfaces -mgz -noaparc -aseg filled -T1 brain.finalsurfs $subj rh, and it worked great.

Running the same command using version 6 (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) I get this error: “… generating cortex label... 1 non-cortical segments detected only using segment with 71880 vertices LabelErode: NULL label No such file or directory LabelDilate: NULL label No such file or directory Segmentation fault: 11”

When changing the command to ( mris_make_surfaces -mgz -noaparc -noaseg -T1 brain.finalsurfs $subj rh ) it runs without error. However, the result is clearly not as good - the pial surface looks like a slightly extended/inflated white surface. This is also true for a brain that worked perfectly with version 5.3.

From the error I am guessing that labels in filled (127 and 255) are not those required. Is it (still) possible to use filled.mgz as the input to -aseg in mris_make_surfaces? Is it perhaps possible to modify the label numbers in filled.mgz to get this working again?

Thanks, Scott