Hmmm, I'm not sure what is going on either. The problem seems to be that the file is not getting unzipped (and so does not have anything to do with the switch statement per se).
Sarina, try going into matlab and running
a = MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz');
and let me know if that works or whether it generates the same error
doug
On 07/29/2014 01:22 PM, Marie Schaer wrote:
Hi Sarina,
Thanks for the log, I see better the problem. However I unfortunately don't know the answer. The lGI calls MRIread and load_mgh, and the error seems to related to load_mgh.m itself.
Bruce / Doug / Nick, any guess what can yield such a "switch expression must be a scalar or string constant" error in load_mgh? (full log attached in Sarina's previous email)
Thanks a lot,
Marie
On Jul 29, 2014, at 3:29 AM, Sarina Iwabuchi <Sarina.Iwabuchi@nottingham.ac.uk mailto:Sarina.Iwabuchi@nottingham.ac.uk> wrote:
Hi Marie, I've attached the log file. Thanks very much, Sarina Iwabuchi
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Hi Sarina,
Can you please send me the full log of the LGI (e.g. recon-all.log) for this subject?
Thanks,
Marie
On Jul 28, 2014, at 7:23 AM, "Sarina Iwabuchi" <Sarina.Iwabuchi at nottingham.ac.uk https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<mailto:Sarina.Iwabuchi at nottingham.ac.uk https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> wrote:
Hi all,
I have been trying to run localGI and have been coming across errors. It creates the filled.mgz file and opens matlab (running 2012a) but crashes straight after with the below errors:
/ reading filled volume...
/set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant.
Error in load_mgh (line 158) switch type
Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Error in make_outer_surface (line 24) vol=MRIread(filled_volume);
Has anyone come across this? I do have gunzip on my system.
Thanks very much,
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU
<recon-all.log>
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