Re: [Freesurfer] fast_selxavg3 error when Octave is used
After installing the io package textread works. Sent from Mail for Windows 10 From: Douglas N Greve Sent: Saturday, January 30, 2016 2:06 AM To: m.abouelya...@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.abouelya...@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.abouelya...@gmail.com <mailto:m.abouelya...@gmail.com> > *Sent: *Friday, January 29, 2016 12:01 PM > *To: *Douglas Greve <mailto:gr...@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:gr...@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 11:41 AM > *To: *m.abouelya...@gmail.com <mailto:m.abouelya...@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.abouelya...@gmail.com > <mailto:m.abouelya...@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:gr...@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 11:27 AM > *To: *m.abouelya...@gmail.com <mailto:m.abouelya...@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.abouelya...@gmail.com > <mailto:m.abouelya...@gmail.com> wrote: > > Yes, it exists in the location you mentioned… > > > *From: *Douglas N Greve <mailto:gr...@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.abouelya...@gmail.com > <mailto:m.abouelya...@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> > &g
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.abouelya...@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.abouelya...@gmail.com <mailto:m.abouelya...@gmail.com> > *Sent: *Friday, January 29, 2016 12:01 PM > *To: *Douglas Greve <mailto:gr...@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:gr...@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 11:41 AM > *To: *m.abouelya...@gmail.com <mailto:m.abouelya...@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.abouelya...@gmail.com > <mailto:m.abouelya...@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:gr...@nmr.mgh.harvard.edu> > *Sent: *Friday, January 29, 2016 11:27 AM > *To: *m.abouelya...@gmail.com <mailto:m.abouelya...@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.abouelya...@gmail.com > <mailto:m.abouelya...@gmail.com> wrote: > > Yes, it exists in the location you mentioned… > > > *From: *Douglas N Greve <mailto:gr...@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.abouelya...@gmail.com > <mailto:m.abouelya...@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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > &g
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.abouelya...@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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] fast_selxavg3 error when Octave is used
Yes, it exists in the location you mentioned… From: Douglas N Greve Sent: Friday, January 29, 2016 2:27 AM To: 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.abouelya...@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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
[Freesurfer] fast_selxavg3 error when Octave is used
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 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.
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.abouelya...@gmail.com wrote: Yes, it exists in the location you mentioned… *From: *Douglas N Greve <mailto:gr...@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.abouelya...@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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
Re: [Freesurfer] fast_selxavg3 error when Octave is used
yes On 1/28/16 9:31 PM, m.abouelya...@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:gr...@nmr.mgh.harvard.edu> *Sent: *Friday, January 29, 2016 11:27 AM *To: *m.abouelya...@gmail.com <mailto:m.abouelya...@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.abouelya...@gmail.com <mailto:m.abouelya...@gmail.com> wrote: Yes, it exists in the location you mentioned… *From: *Douglas N Greve <mailto:gr...@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.abouelya...@gmail.com <mailto:m.abouelya...@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 gr...@nmr.mgh.harvard.edu <mailto:gr...@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. ___ Freesurfer mailing list 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.
