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
From: Linn Mittlestein linnmittle@gmail.comDate: Fri, Oct 18, 2013 at 1:30 PM Subject: LGI path problem To: 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
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 linnmittle@gmail.com Date: Mon, Oct 21, 2013 at 9:33 AM Subject: Fwd: LGI path problem To: freesurfer@nmr.mgh.harvard.edu
From: Linn Mittlestein linnmittle@gmail.comDate: Fri, Oct 18, 2013 at 1:30 PM Subject: LGI path problem To: 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
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 <linnmittle@gmail.commailto:linnmittle@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 <linnmittle@gmail.commailto:linnmittle@gmail.com> Date: Mon, Oct 21, 2013 at 9:33 AM Subject: Fwd: LGI path problem To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
From: Linn Mittlestein <linnmittle@gmail.commailto:linnmittle@gmail.com>Date: Fri, Oct 18, 2013 at 1:30 PM Subject: LGI path problem To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.
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.
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.Schaer@unige.chwrote:
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 linnmittle@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 linnmittle@gmail.com Date: Mon, Oct 21, 2013 at 9:33 AM Subject: Fwd: LGI path problem To: freesurfer@nmr.mgh.harvard.edu
From: Linn Mittlestein linnmittle@gmail.comDate: Fri, Oct 18, 2013 at 1:30 PM Subject: LGI path problem To: 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 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.
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 <linnmittle@gmail.commailto:linnmittle@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.comhttp://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.Schaer@unige.chmailto:Marie.Schaer@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 <linnmittle@gmail.commailto:linnmittle@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 <linnmittle@gmail.commailto:linnmittle@gmail.com> Date: Mon, Oct 21, 2013 at 9:33 AM Subject: Fwd: LGI path problem To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
From: Linn Mittlestein <linnmittle@gmail.commailto:linnmittle@gmail.com>Date: Fri, Oct 18, 2013 at 1:30 PM Subject: LGI path problem To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.
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.Schaer@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 linnmittle@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.
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.Schaer@unige.chwrote:
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 linnmittle@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 linnmittle@gmail.com Date: Mon, Oct 21, 2013 at 9:33 AM Subject: Fwd: LGI path problem To: freesurfer@nmr.mgh.harvard.edu
From: Linn Mittlestein linnmittle@gmail.comDate: Fri, Oct 18, 2013 at 1:30 PM Subject: LGI path problem To: 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 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.
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 <linnmittle@gmail.commailto:linnmittle@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.Schaer@unige.chmailto:Marie.Schaer@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 <linnmittle@gmail.commailto:linnmittle@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.comhttp://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.Schaer@unige.chmailto:Marie.Schaer@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 <linnmittle@gmail.commailto:linnmittle@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 <linnmittle@gmail.commailto:linnmittle@gmail.com> Date: Mon, Oct 21, 2013 at 9:33 AM Subject: Fwd: LGI path problem To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
From: Linn Mittlestein <linnmittle@gmail.commailto:linnmittle@gmail.com>Date: Fri, Oct 18, 2013 at 1:30 PM Subject: LGI path problem To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.
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.Schaer@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 linnmittle@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.Schaer@unige.chwrote:
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 linnmittle@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.
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.Schaer@unige.chwrote:
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 linnmittle@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 linnmittle@gmail.com Date: Mon, Oct 21, 2013 at 9:33 AM Subject: Fwd: LGI path problem To: freesurfer@nmr.mgh.harvard.edu
From: Linn Mittlestein linnmittle@gmail.comDate: Fri, Oct 18, 2013 at 1:30 PM Subject: LGI path problem To: 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
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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.Schaer@unige.ch mailto:Marie.Schaer@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 <linnmittle@gmail.com <mailto:linnmittle@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.Schaer@unige.ch <mailto:Marie.Schaer@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 <linnmittle@gmail.com <mailto:linnmittle@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.Schaer@unige.ch <mailto:Marie.Schaer@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 <linnmittle@gmail.com <mailto:linnmittle@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* <linnmittle@gmail.com <mailto:linnmittle@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* <linnmittle@gmail.com <mailto:linnmittle@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.
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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.
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Linn Mittlestein -
Marie Schaer