External Email - Use Caution
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