While I fix the virtual machine issues, I tried to use freesurfer on a cluster machine which has matlab and FSL. Problem is, when I executed fast_selxavg3 preprocessing is done but when matlab gets started it gives me a message of matlab command not found.
When I type matlab in the terminal it works perfectly and the Freesurfer path is included in matlab.
I had all the paths for all dependencies checked like FSLDIR and FREESURFER_HOME.
The error comes from these lines in selxavg3-sess LINE 313: echo "------------------------------------------" >> $LF cat $MLF >> $LF echo "------------------------------------------" >> $LF
if(! $monly && $nprocs > 0) then echo "------------------------------------------" | tee -a $LF if($UseOctave == 0) then echo "------- matlab output --------------------" | tee -a $LF cat $MLF | matlab -display iconic | tee -a $LF else echo "------- octave output --------------------" | tee -a $LF echo LD_LIBRARY_PATH $LD_LIBRARY_PATH cat $MLF | $FS_OCTAVE_BIN |& tee -a $LF endif echo "------------------------------------------" | tee -a $LF rm $MLF if(! -e $okfile) then echo "ERROR: fast_selxavg3() failed\n"; exit 1; endif
I tried matlab -display iconic which started matlab in the command line normally. However, it gives this warning Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. Can this be the problem? The cluster I am working on is the one without a proper GPU processing unit so I don’t use Freeview on it.
Thank you, Best, Mohamed
From: Douglas N Greve Sent: Saturday, January 30, 2016 2:06 AM To: m.abouelyazid@gmail.com; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fast_selxavg3 error when Octave is used
Does octave now have a version of textread? I looked over my notes and saw that it did not support it at one point, which I apparently forgot and put it into the code. Can't do much about your space issue
On 01/29/2016 11:37 AM, m.abouelyazid@gmail.com wrote:
Okaii, so I fixed that last issue by changing the version of octave installed then I found I needed to install FSL also. Problem is… now the virtual machine drive has run out of space…
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*From: *m.abouelyazid@gmail.com mailto:m.abouelyazid@gmail.com *Sent: *Friday, January 29, 2016 12:01 PM *To: *Douglas Greve mailto:greve@nmr.mgh.harvard.edu *Subject: *RE: [Freesurfer] fast_selxavg3 error when Octave is used
Are there any other paths that I need to add? because now I get another error
Extension format = nii.gz
error: `textread' undefined near line 210 column 17
error: evaluating argument list element number 1
error: evaluating argument list element number 1
error: called from:
error: /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m at line 210, column 10
error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line 53, column 9
*From: *Douglas Greve mailto:greve@nmr.mgh.harvard.edu *Sent: *Friday, January 29, 2016 11:41 AM *To: *m.abouelyazid@gmail.com mailto:m.abouelyazid@gmail.com; free surfer mailto:freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used
yes
On 1/28/16 9:31 PM, m.abouelyazid@gmail.com mailto:m.abouelyazid@gmail.com wrote:
I am running on the virtual machine where I don’t have MATLAB so I installed Octave… Maybe I should include the folder into the Octave path? *From: *Douglas Greve <mailto:greve@nmr.mgh.harvard.edu> *Sent: *Friday, January 29, 2016 11:27 AM *To: *m.abouelyazid@gmail.com <mailto:m.abouelyazid@gmail.com>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used Is that directory in your matlab path? does it run properly in matlab? On 1/28/16 8:36 PM, m.abouelyazid@gmail.com <mailto:m.abouelyazid@gmail.com> wrote: Yes, it exists in the location you mentioned… *From: *Douglas N Greve <mailto:greve@nmr.mgh.harvard.edu> *Sent: *Friday, January 29, 2016 2:27 AM *To: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used Does fast_fileexists.m exist in $FREESURFER_HOME/fsfast/toolbox ? On 01/28/2016 07:16 AM, m.abouelyazid@gmail.com <mailto:m.abouelyazid@gmail.com> wrote: > > Since I am a windows user I got the Virtualbox version of FreeSurfer > and to use fs fast, I installed Octave on the virtual machine, I set > the environment variables and then when I run the command > > selxavg3-sess -analysis rtopy.lh -sf sessid > > which runs a retinotopy analysis, I get the following error: > > sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx > > sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -analysis > rtopy.lh -sf sessid > > error: `fast_fileexists' undefined near line 5 column 4 > > ------------------------------------------ > > ERROR: fast_selxavg3() failed\n > > Any idea of the cause of this error and how to run around? > > Thank you, > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://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.