Are you in the 'surf' directory? If not, then do "-overlay
$subject/surf/lh.pial_lgi"
On 11/05/2013 11:26 AM, Linn Mittlestein wrote:
Hi,
Thank you very much, it works. I now however have another problem
(sorry!). I have run the command on test subject and want to display
using tksurfer. The file lh.pial_lgi has for sure been created, and i
cd into correct subjects directory however when I try tksurfer XXXX lh
inflated -overlay lh.pial_lgi I get following error: ERROR: cannot
find lh.pial_lgi
Any ideas?
Kind Regards,
Linn
On Mon, Oct 28, 2013 at 6:46 PM, Marie Schaer <marie.sch...@unige.ch
<mailto:marie.sch...@unige.ch>> wrote:
Hi Linn,
We have an issue using lGI with matlab 2013 in the current
version. It will be updated in the new version, but in the mean
time if you want to use it, it's a very small change that you have
to do. See the following post:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html
Or there is a note on LGI and matlab 2013 in the "Release Notes"
page on the wiki.
Hope it works, let me know,
Marie
On Oct 28, 2013, at 3:38 AM, Linn Mittlestein
<linnmit...@gmail.com <mailto:linnmit...@gmail.com>> wrote:
Dear Marie,
Thank you, I use bash and changed my .bashrc and this worked, I
previously had used wrong syntax. Thank you very much for your
help. However, I now recieve another error and do not know what
it means at all. I copy in the error ! Thank you.
Improper assignment with rectangular empty matrix.
Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));
Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);
Error in reorganize_verticeslist (line 28)
[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));
Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A,
mesh_outer, perim,
verticeslist, step);
>>
ERROR: make_roi_paths did not complete successfully!
On Wed, Oct 23, 2013 at 4:04 PM, Marie Schaer
<marie.sch...@unige.ch <mailto:marie.sch...@unige.ch>> wrote:
Hi Linn,
If you are using tcsh, you have to edit the file $HOME/.cshrc
(.shrc should work as well) to add the following line:
setenv PATH $PATH:/YOUR_PATH_TO_MATLAB_BIN_DIRECTORY
Then close the terminal and open a new one. Use the env
command to be sure that your path has been modified, then the
getmatlab command from FreeSurfer should give you the correct
location.
Best,
Marie
On Oct 23, 2013, at 12:23 AM, Linn Mittlestein
<linnmit...@gmail.com <mailto:linnmit...@gmail.com>>
wrote:
Hi, thank you. I am using Linux. I not sure where to change
path, ie which file this should be done in and where this
file is located. This the error message I recieve, and as I
said It is launching the wrong matlab and I don't know how
change this.
Launching Matlab7p13
Warning: Unable to open display 'iconic'. You will not be
able to display graphics on the screen.
< M A T L A B (R) >
Copyright 1984-2011 The MathWorks, Inc.
R2011b (7.13.0.564) 32-bit (glnx86)
August 13, 2011
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com
<http://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
'/x/x/x/x/2/x/x/x/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!
Linux 2.6.32-358.2.1.el6.x86_64 #1 SMP Tue Mar 12 14:18:09
CDT 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj exited with ERRORS at Wed Oct 23 08:20:58
BST 2013
Thank you very much for your time and help,
Kind Regards,Linn
On Tue, Oct 22, 2013 at 10:50 PM, Marie Schaer
<marie.sch...@unige.ch <mailto:marie.sch...@unige.ch>> wrote:
Hi Linn,
Sorry for the delay in answering. The path has to be set
directly in your environment variable (the variable
$PATH has to point to the correct version). I need a few
more details about what you tried and which OS you are
using to be able to help you.
If you are using mac, here is an example on how you can
set the path in the .shrc file:
setenv PATH $PATH":/Applications/MATLAB_R2013b.app/bin"
You can also have a look at the following posts:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07283.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26909.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27290.html
Let me know how it goes,
Marie
On Oct 22, 2013, at 2:41 AM, Linn Mittlestein
<linnmit...@gmail.com <mailto:linnmit...@gmail.com>>
wrote:
Hi,
I am trying to compute lgi measures, and I think my
problem lies in the fact that the matlab path is not
set correctly; it is calling an older version of matlab
however I need it to point to matlab2013b. I have tried
numerous things like changing the startup.m file, the
.bashrc file and exporting the matlab path, however It
keeps calling another version of Matlab. Can someone
please tell me how exactly the path is set and where?
Best Wishes and thank you,
Linn
---------- Forwarded message ----------
From: *Linn Mittlestein* <linnmit...@gmail.com
<mailto:linnmit...@gmail.com>>
Date: Mon, Oct 21, 2013 at 9:33 AM
Subject: Fwd: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
From: *Linn Mittlestein* <linnmit...@gmail.com
<mailto:linnmit...@gmail.com>>Date: Fri, Oct 18, 2013
at 1:30 PM
Subject: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Hi,
I am trying to compute lgi measures, and I think my
problem lies in the fact that the matlab path is not
set correctly; it is calling an older version of matlab
however I need it to point to matlab2013b. I have tried
numerous things like changing the startup.m file, the
.bashrc file and exporting the matlab path, however It
keeps calling another version of Matlab. Can someone
please tell me how exactly the path is set and where?
Best Wishes and thank you,
Linn
_______________________________________________
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.
_______________________________________________
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.
