Hi Jon,
I guess you don't have the image processing toolbox installed with matlab?
fspecial is a matlab function comprised in this toolbox… I am afraid that lGI
with not run without it.
Marie
On Mar 18, 2013, at 12:03 PM, Jon Wieser <wie...@uwm.edu>
wrote:
> I added the matlab bin directory to my PATH.
>
>
> getmatlab
> /Applications/MATLAB_R2012b.app/bin/matlab
>
>
>
> I ran :
> recon-all -s freesurfer -localGI
> and got the following:
>
> Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0001
> Actual FREESURFER_HOME /Applications/freesurfer
> -rw-rw-rw- 1 wieser admin 450426 Mar 18 13:58
> /Studies/MJMRI/MJ0001/freesurfer/scripts/recon-all.log
> Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue
> Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
> /Studies/MJMRI/MJ0001/freesurfer/surf
> #--------------------------------------------
> #@# Local Gyrification Index lh Mon Mar 18 13:59:36 CDT 2013
> \n mris_compute_lgi --i lh.pial \n
> =================
> rm -Rf /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial
> =================
> =================
> mkdir -p /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial
> =================
> =================
> mris_fill -c -r 1 lh.pial
> /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
> =================
> reading surface from lh.pial...
> writing filled volume to
> /Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
> conforming output volume
> setting resolution for intermediate calculations to 1.0000
> =================
> make_outer_surface('/Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
> exit
> =================
>
> < M A T L A B (R) >
> Copyright 1984-2012 The MathWorks, Inc.
> R2012b (8.0.0.783) 64-bit (maci64)
> August 22, 2012
>
>
> To get started, type one of these: helpwin, helpdesk, or demo.
> For product information, visit www.mathworks.com.
>
>>> reading filled volume...
> closing volume...
> Undefined function 'fspecial' for input arguments of type 'char'.
>
> Error in make_outer_surface (line 31)
> Gaussian = fspecial('gaussian',[2 2],1);
>
>>>
> ERROR: make_outer_surface did not create output file
> '/Studies/MJMRI/MJ0001/freesurfer/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
> Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue
> Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
>
> recon-all -s freesurfer exited with ERRORS at Mon Mar 18 13:59:49 CDT 2013
>
> For more details, see the log file
> /Studies/MJMRI/MJ0001/freesurfer/scripts/recon-all.log
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
>
>
>
>
>
>
> ----- Original Message -----
> From: "Marie Schaer" <marie.sch...@unige.ch>
> To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu>
> Sent: Monday, March 18, 2013 1:07:54 PM
> Subject: Re: [Freesurfer] LGI
>
>
>
>
>
>
> Hi Jon,
>
>
> It looks like the matlab path is not set on your machine. Can you set the
> $PATH environment variable to include the path to the matlab functions as
> well? You can try to launch the command "getmatlab", if you get the answer
> that matlab is not installed, it means that the $PATH environment variable is
> not properly set. You can also look on the mailing list, there are a few
> explanations about this path issue, among which the following one:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html
>
>
>
> Let me know if you don't find how to make it work.
>
>
> Best,
>
>
> Marie
>
>
>
>
> On Mar 18, 2013, at 10:44 AM, Jon Wieser < wie...@uwm.edu >
> wrote:
>
>
> i am trying to computer the LGI local gyrification index with freesurfer. I
> have Matlab on my machine.
> I got the following error:
>
>
> recon-all -s freesurfer -localGI
> Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012
> Actual FREESURFER_HOME /Applications/freesurfer
> -rw-rw-r-- 1 wieser admin 506264 Mar 18 12:37
> /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log
> Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue
> Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
> /Studies/MJMRI/MJ0012/freesurfer/surf
> #--------------------------------------------
> #@# Local Gyrification Index lh Mon Mar 18 12:43:04 CDT 2013
> \n mris_compute_lgi --i lh.pial \n
> ERROR: Matlab is required to run mris_compute_lgi!
> Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue
> Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
>
> recon-all -s freesurfer exited with ERRORS at Mon Mar 18 12:43:04 CDT 2013
>
> For more details, see the log file
> /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
> JOn
>
> --
> Jon Wieser
> Research Specialist
> UW-Milwaukee
> Psychology Department, Pearse Hall Rm 366
> 2441 East Hartford Ave
> Milwaukee, WI 53211
> Phone: 414-229-7145
> Fax: 414-229-5219
> _______________________________________________
> 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.
>
> --
> Jon Wieser
> Research Specialist
> UW-Milwaukee
> Psychology Department, Pearse Hall Rm 366
> 2441 East Hartford Ave
> Milwaukee, WI 53211
> Phone: 414-229-7145
> Fax: 414-229-5219
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
