Re: [Freesurfer] FreeSurfer LocalGI error

Thank you very much, Dear Andrew! for your expert advise. I really appreciated. Its worked. Best Regards Manoj On Tue, Jan 16, 2018 at 10:39 PM, Hoopes, Andrew wrote: > Hi Manoj, > > This probably has to do with SIP being enabled, which blocks libraries > stored in

Re: [Freesurfer] FreeSurfer LocalGI error

Hi Manoj, This probably has to do with SIP being enabled, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best, Andrew On Jan 16, 2018, at

[Freesurfer] FreeSurfer LocalGI error

Hello Dear FreeSurfer Experts, I am trying to run "recon-all -s subject -localGI" command on my Mac bash terminal. I am getting following error. I am using using Freesurfer V 6.0 and running on MacOS High Sierra (version 10.13) I also run the istallation update :"sudo -E fs_update" as per

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Doug, I get the following error: Undefined function 'MRIread' for input arguments of type 'char'. Sarina On 29 Jul 2014, at 18:34, Douglas N Greve wrote: a = MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz'); Sarina Iwabuchi Division

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Sarina, you need to have $FREESURFER_HOME/matlab in your matlab path. Try: addpath(sprintf('%s/matlab', getenv('FREESURFER_HOME'))) cheers Bruce On Wed, 30 Jul 2014, Sarina Iwabuchi wrote: Hi Doug, I get the following error: Undefined function 'MRIread' for input arguments of type

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Bruce, It still shows the same error: 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)

Re: [Freesurfer] LocalGI error {Disarmed}

Is gunzip in your path? When you open a shell and type which gunzip what is printed out? On 07/30/2014 10:45 AM, Sarina Iwabuchi wrote: Hi Bruce, It still shows the same error: set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set:

Re: [Freesurfer] LocalGI error {Disarmed}

And in matlab, what do you get if you type unix('which gunzip') On 07/30/2014 11:08 AM, Sarina Iwabuchi wrote: I get: /usr/bin/gunzip On 30 Jul 2014, at 15:58, Douglas N Greve wrote: Is gunzip in your path? When you open a shell and type which gunzip what is printed out? On

Re: [Freesurfer] LocalGI error {Disarmed}

set: Variable name must begin with a letter. gunzip: Command not found. ans = 1 On 30 Jul 2014, at 16:27, Douglas N Greve wrote: And in matlab, what do you get if you type unix('which gunzip') On 07/30/2014 11:08 AM, Sarina Iwabuchi wrote: I get: /usr/bin/gunzip On

Re: [Freesurfer] LocalGI error {Disarmed}

OK, so there is something going wrong with your unix environment inside of matlab (this is not a freesurfer problem per se). Is there someone around that you can ask about it? Can someone else try this last command to see if it works? There might be something wrong with the resource file of

Re: [Freesurfer] LocalGI error {Disarmed}

Hi Marie,I've attached the log file.Thanks very much,Sarina Iwabuchi This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not

Re: [Freesurfer] LocalGI error

On 29 Jul 2014, at 11:29, Sarina Iwabuchi wrote: Hi Marie, I've attached the log file. Thanks very much, Sarina Iwabuchi This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error,

Re: [Freesurfer] LocalGI error {Disarmed}

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

Re: [Freesurfer] LocalGI error {Disarmed}

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 =

[Freesurfer] LocalGI error

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.

Re: [Freesurfer] LocalGI error

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.iwabu...@nottingham.ac.ukmailto:sarina.iwabu...@nottingham.ac.uk wrote: Hi all, I have been trying to run localGI and have