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#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 <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
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