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/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 <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
>
> _______________________________________________
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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