I don't think it matters but I would use eye instead of nan for M. But the critical issue is where you get your data and what dimensions it has cheers Bruce
On Fri, 21 Jun 2019, Loïc Daumail wrote:
External Email - Use Caution
Me again,
Also, here is how I save the matrix on matlab:
M = nan(4,4); save_mgh('freeview_overlay', ['/home/loic/Documents/emb_output/mgh_format/lh_emb_' char(subjectsList(1)) '_' char(statesList(1)) '.mgz'], M); Thanks,
Sincerely,
Loïc
Le ven. 21 juin 2019 à 12:25, Loïc Daumail loic.daumail@gmail.com a écrit : 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#Sig... 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/lin ux-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 fischl@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.daumail@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.daumail@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+ml@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.daumail@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+ml@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 <fischl@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 > <fischl@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 < > > > fischl@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.daumail@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