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…

> Sent from Mail <http://go.microsoft.com/fwlink/?LinkId=550986> for

> Windows 10

> *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: 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

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Douglas N. Greve, Ph.D.

MGH-NMR Center

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

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