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 CautionAfaik 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 CautionHi 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 subsetsof
fsaverage) On Mon, 20 May 2019, Loïc Daumail wrote: > > External Email - Use Caution > > Hi Bruce, > > Thanks for your response. Is it also fine for fsaverage5surface 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 andthreshold 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 performingdiffusion embedding map
on fMRI > data. > > > > I am now using the SurfStat toolbox(Matlab) in orderto obtain p-value maps to
compare > between > > two groups. > > > > After obtaining the p-value map, I would like to labelthe 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 SurfStatPoutput p-value map?
> > How would you do it, (tools to convert into a specificformat, surfaces and
atlas to > load on > > Freeview, which format for those ones)? > > I would be very grateful if you could detail a bit, asI 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
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