External Email - Use Caution Hi Bruce,
Thanks for your tip. Unfortunately, I am still running through an error... I have a matrix of 18715 elements regarding both hemispheres. The size of fsaverage5 is 20484 I believe, so I filled the remaining elements with zeros, and also tried with rand(). The other issue is that I am not so sure which part of the matrix is for lh and the other one for rh. Thus, I divided 18715/2 and took the 9357 first elements of the 18715 matrix. Then filled it with zeros or random values to reach 10242. Then I saved it with save_mgh function and tried to load it with freeview using the following command line: freeview -f ~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh_format/lh_emb_sub-002_compassion.mgz I am getting the following error: " Did not find any volume info 2 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named loic-HP-ZBook-17 by loic Fri Jun 21 12:15:53 2019 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0" Any idea of what could be wrong in my process? Thanks Sincerely, Loïc Le jeu. 20 juin 2019 à 19:39, Bruce Fischl <fis...@nmr.mgh.harvard.edu> a écrit : > Hi Loïc > > the .mgz file should having dimensions nvertices x 1 x 1 for freeview to > know it is a surface overlay I believe > > cheers > Bruce > > > > On Thu, 20 Jun 2019, Loïc Daumail wrote: > > > > > External Email - Use Caution > > > > Hi Bruce, > > > > I am reaching out to you, as I am trying to load the surface scalar > values of diffusion embedding > > for overlay on a pial surface in Freeview. > > > > I used save_mgh to save a scalar matrix containing surface embedding > values in an .mgz format. > > However I can't load it in freeview, be either only half of the matrix > data (one hemisphere I > > assume) or the whole matrix saved in the same file. > > > > Is there anything specific I need to do in order to be able to visualize > a scalar overlay on a > > surface? Is .mgz a wrong format for scalar values? I also tried with > .nii.gz, or .mgh. I am not even > > sure save_mgh can do all this... > > > > Thanks in advance, > > > > Sincerely, > > > > Loïc > > > > > > > > Le lun. 27 mai 2019 à 11:54, Loïc Daumail <loic.daum...@gmail.com> a > écrit : > > Hi Tim, > > > > Your link works perfectly, it's awesome! > > Thanks a lot, > > > > Best, > > > > Loïc > > > > Le lun. 27 mai 2019 à 11:43, Loïc Daumail <loic.daum...@gmail.com> a > écrit : > > Hi Tim, > > > > 'mean_rest' is a diffusion embedding map, which contains scores for > every vertex on > > fsaverage5 surface resolution. > > 'surf.b' is the pial surface of both hemispheres of fsaverage5... I also > tried forjust > > lh hemisphere, but it gives me the same result... > > > > Thanks for the link! > > > > Best, > > > > Loïc > > > > Le lun. 27 mai 2019 à 11:20, Tim Schäfer <ts...@rcmd.org> a écrit : > > External Email - Use Caution > > > > Hi Loïc, > > > > that does not look correct, the data is definitely off. I'm not > sure where > > the variables `mean_rest` and `surf.b` come from in your code, and > I suspect > > that something is wrong with them. > > > > In the meantime, I got interested in this myself and put together > some code > > that will load the Desikan data for both hemispheres and display > it in > > surfstat. Feel free to use it, there also is an example screenshot > of the > > results: > > > > > > > https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desikan > > > > Best, > > > > Tim > > > > -- > > Dr. Tim Schäfer > > Postdoc Computational Neuroimaging > > Department of Child and Adolescent Psychiatry, Psychosomatics and > > Psychotherapy > > University Hospital Frankfurt, Goethe University Frankfurt am > Main, Germany > > > > > On May 27, 2019 at 11:01 AM Loïc Daumail <loic.daum...@gmail.com> > wrote: > > > > > > > > > External Email - Use Caution > > > > > > Hi Tim, > > > > > > Thanks a lot for your help, indeed, this is exactly what I > needed! > > > I wrote this : > > > " > > > subjects_dir = > '/home/loic/Documents/recon_all_success/freesurfer/'; > > > subject_id = 'sub-004'; > > > hemi = 'lh'; > > > > > > aparc_file_this_hemi = fullfile(subjects_dir, subject_id, > 'label', > > > sprintf("%s.aparc.annot", hemi)); > > > [vertices, label, colortable] = > read_annotation(aparc_file_this_hemi); > > > fprintf("Read aparc parcellation file '%s' containing %d > regions.\n", > > > aparc_file_this_hemi, length(colortable.struct_names)); > > > for sidx = 1:length(colortable.struct_names) > > > region = colortable.struct_names{sidx}; > > > struct_code = colortable.table(sidx, 5); > > > vertices_of_struct_roi = find(label == struct_code); > > > fprintf("Found region '%s' with %d verts.\n", region, > > > length(vertices_of_struct_roi)); > > > end > > > fig1 = figure(); > > > SurfStatView(mean_rest, surf.b); > > > SurfStatColormap(colortable.table(:,1:3)/255); > > > " > > > However, the image I obtain seems a bit fuzzy...( see attached) > > > Is it because of my data? > > > > > > Thanks in advance, > > > > > > Loïc > > > > > > > > > Le jeu. 23 mai 2019 à 17:20, Tim Schäfer <ts...@rcmd.org> a > écrit : > > > > > > > External Email - Use Caution > > > > > > > > Afaik SurfStat is not maintained anymore and I think it's been > this way > > > > for quite a while now. Maybe someone else knows better? > > > > > > > > The website is at http://www.math.mcgill.ca/keith/surfstat/ > and it says > > > > 'Updated 26 September 2008'. I'm not sure whether that's > really true, > > but > > > > at least for the last 14 months (the only time frame I know > about), > > there > > > > have not been any changes to that website or any new releases > of > > SurfStat. > > > > > > > > Tim > > > > > > > > > On May 23, 2019 at 4:36 PM Bruce Fischl < > fis...@nmr.mgh.harvard.edu> > > > > wrote: > > > > > > > > > > > > > > > Hi Loic > > > > > > > > > > sorry, can you ask whoever maintains surfstat? Or maybe > someone else > > on > > > > the > > > > > list knows? I don't. You can label surfaces manually with > the dev > > > > version > > > > > of freeview if you want. > > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > > > > > > On Thu, 23 May 2019, Loïc > > > > > Daumail wrote: > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > Hi Bruce, > > > > > > > > > > > > I am coming back to this request as I was wondering: > > > > > > would it be possible to load freesurfer surface atlases in > surfstat > > in > > > > order to label my surfaces? > > > > > > Is their format compatible? I saw surfstat only accepts a > limited > > > > array of formats... > > > > > > > > > > > > Thanks, > > > > > > Best, > > > > > > > > > > > > Loïc > > > > > > > > > > > > Le lun. 20 mai 2019 à 16:15, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu> > > > > a écrit : > > > > > > sure. All the fsaverages are in the same space (they > are > > subsets > > > > of > > > > > > fsaverage) > > > > > > On Mon, 20 May 2019, Loïc Daumail wrote: > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > Hi Bruce, > > > > > > > > > > > > > > Thanks for your response. Is it also fine for > fsaverage5 > > > > surface or I need to switch > > > > > > my data to > > > > > > > fsaverage? > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > Sincerely, > > > > > > > > > > > > > > Loïc > > > > > > > > > > > > > > Le lun. 20 mai 2019 à 15:52, Bruce Fischl < > > > > fis...@nmr.mgh.harvard.edu> a écrit : > > > > > > > Hi Loic > > > > > > > > > > > > > > if you are on the fsaverage surface you can > save the > > > > -log10(p) values > > > > > > > using save_mgh.m, then load them in freeview > and > > > > threshold them or > > > > > > > whatever > > > > > > > > > > > > > > cheers > > > > > > > Bruce > > > > > > > On Mon, 20 May 2019, Loïc Daumail wrote: > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > Also, one more thing: > > > > > > > > > > > > > > > > My data is on fsaverage5 resolution. > > > > > > > > > > > > > > > > Thanks in advance, > > > > > > > > > > > > > > > > Sincerely, > > > > > > > > > > > > > > > > Loïc > > > > > > > > > > > > > > > > Le lun. 20 mai 2019 à 09:49, Loïc Daumail < > > > > loic.daum...@gmail.com> a écrit : > > > > > > > > Dear Freesurfer community, > > > > > > > > > > > > > > > > I obtained score matrices of surfaces after > > performing > > > > diffusion embedding map > > > > > > on fMRI > > > > > > > data. > > > > > > > > > > > > > > > > I am now using the SurfStat > toolbox(Matlab) in order > > > > to obtain p-value maps to > > > > > > compare > > > > > > > between > > > > > > > > two groups. > > > > > > > > > > > > > > > > After obtaining the p-value map, I would > like to > > label > > > > the surface in order to > > > > > > > identify the > > > > > > > > regions of significant difference between > both > > groups. > > > > > > > > > > > > > > > > Would it be possible to use Freview in > order to do > > it? > > > > > > > > If so, which format should I use for my > SurfStatP > > > > output p-value map? > > > > > > > > How would you do it, (tools to convert > into a > > specific > > > > format, surfaces and > > > > > > atlas to > > > > > > > load on > > > > > > > > Freeview, which format for those ones)? > > > > > > > > I would be very grateful if you could > detail a bit, > > as > > > > I am new to these > > > > > > tools! > > > > > > > > > > > > > > > > Thanks in advance, > > > > > > > > > > > > > > > > Loïc Daumail > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > > > > Dr. Tim Schäfer > > > > Postdoc Computational Neuroimaging > > > > Department of Child and Adolescent Psychiatry, Psychosomatics > and > > > > Psychotherapy > > > > University Hospital Frankfurt, Goethe University Frankfurt am > Main, > > Germany > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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