External Email - Use Caution 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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