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
