Many thanks for your reply Marie. "getmatlab" returns "ERROR: Cannot find matlab. Does not exist or is not in path."
There is a matlab folder in my Virtualbox installation of FS, at the path /usr/local/freesurfer/matlab, however it only contains .m files rather than the software itself. Among those files, the make_outer_surface function has a date stamp of 2007/11/14, with no other version information. I did a search in /usr/local, and that one seems to be the only copy of make_outer_surface, so there probably isn't any duplicate elsewhere. On my Windows PC I have Matlab 2010a. Can the localGI functions in any way be pointed to it? If not, then could this be done via FSL (on FMRIB cluster) maybe? So far I ran my recons through FSL, then did further analyses locally. When I type matlab in my FSL terminal, it says "MATLAB not allowed on this host. Run inteactive sessions on your local computer or processing jobs on the cluster". On the other hand, if I double click on /usr/local/bin/matlab2006a (in my FSL connection), the 2006a version of Matlab starts up, and seems to be working fine! What do you make of this? Thanks again! Tudor On 14 June 2013 17:31, Marie Schaer <marie.sch...@unige.ch> wrote: > > > 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 <gr...@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 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 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > >
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