Hi Tudor, the lGI stream definitely uses matlab, so that will be a problem at some point if not now. I would have thought that it would have reported that it could not find matalb. Marie would know for sure.
doug
On 6/14/13 3:25 AM, Tudor Popescu wrote:
Dear Freesurfer & localGI experts,
I want to compare local GI (gyrification index) between my two groups. Following the help https://surfer.nmr.mgh.harvard.edu/fswiki/LGI, I ran this command for one of my subjects:
recon-all -s M01 -localGI
but it resulted in the error:
make_outer_surface('/media/math/all38subj/M01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/media/math/all38subj/M01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= ERROR:: Too many arguments.
Someone previously http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23414.html received this error due to a space in their path, but I don't specify any path in the above command, and my $SUBJECTS_DIR path doesn't have any spaces or any other dodgy characters.
I'm running FreeSurfer v5.2 from inside Virtualbux/Ubuntu, so Matlab is not included in there, although it exists separately on my Windows partition. I could run recon through FSL, but I don't see any matlab folder there either. Could Matlab be the problem?
Also, which files/folders will I need to delete after I'll have fixed the problem, before re-running the recon for all subjects? Or will it just overwrite any left-overs?
Many thanks in advance for any help! Tudor
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