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, 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 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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