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> 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> > 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>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> >> 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.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> >>> 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> >>> Date: Mon, Oct 21, 2013 at 9:33 AM >>> Subject: Fwd: LGI path problem >>> To: freesurfer@nmr.mgh.harvard.edu >>> >>> >>> >>> From: Linn Mittlestein <linnmit...@gmail.com>Date: 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. >>> >>> >>> >> >> > >
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