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.daum...@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 <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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