Hi Tudor,
Yes you will need matlab with the image processing toolbox installed. The issue may be that you are running FreeSurfer in a virtual machine, with matlab not installed there. But, as Doug mentioned, I would assume the algorithms to answer you that it didn't find matlab.
So, a few ideas: First, try to run getmatlab to see whether you get any answer, and to which matlab it points to. If you have a matlab installed, please let me know which version, as I have had issue with the most recent versions (but not the same issue that you are reporting)
Second, the specific issue of too many or not enough arguments could be found if you have different version of a function with the same name, and the other ones need less arguments. You can use the which function in matlab to see whether this is the case for make_outer_surface.m.
Let me know,
Marie
NB: as for your last question, there is no need to delete anything before rerunning when you will have solved the problem, it will simply overwrite.
On Jun 14, 2013, at 7:20 AM, Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
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 helphttps://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 previouslyhttp://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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