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
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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