Re: [Freesurfer] ROI labels for geometry vertices
Thank you! Although I did not find the exact function you're describing, there is a function with the same name that has the following help: >> help read_annotation [annots] = read_annotation(fname) reads a binary annotation file into a vector or this one >> help freesurfer_read_annotation freesurfer_read_annotation - reads a binary annotation file into a vector [annots] = freesurfer_read_annotation(fname) See also freesurfer_read_surf, freesurfer_read_curv, freesurfer_read_wfile The vector returned has 7-8 digit numbers in it, and they do look like if they can be ROI labels. e.g: >> label(1:1000:1) ans = 9182740 9182740 9182740 9182740 6558940 9182740 9221140 9182740 3957880 14433500 Now how do I tell which ROI these indices correspond to? Thank you! -- Sergey On Dec 7, 2007, at 8:43 PM, Bruce Fischl wrote: Hi Sergey, In matlab you you can use read_annotation.m: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ROI labels for geometry vertices
Thank you! Although I did not find the exact function you're describing, there is a function with the same name that has the following help: >> help read_annotation [annots] = read_annotation(fname) reads a binary annotation file into a vector or this one >> help freesurfer_read_annotation freesurfer_read_annotation - reads a binary annotation file into a vector [annots] = freesurfer_read_annotation(fname) See also freesurfer_read_surf, freesurfer_read_curv, freesurfer_read_wfile The vector returned has 7-8 digit numbers in it, and they do look like if they can be ROI labels. e.g: >> label(1:1000:1) ans = 9182740 9182740 9182740 9182740 6558940 9182740 9221140 9182740 3957880 14433500 Now how do I tell which ROI these indices correspond to? Thank you! -- Sergey On Dec 7, 2007, at 8:43 PM, Bruce Fischl wrote: Hi Sergey, In matlab you you can use read_annotation.m: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ROI labels for geometry vertices
Hi, Please, help me to find out how to extract information I need. For each vertex in the geometry of the cortical surface I want an additional label that tells me which ROI this vertex belongs to. I extract all geometrical information using: mne_read_surfaces in matlab. This, however, does not give me the labels for ROI of each vertex. I plan to use freesurfer atlas for ROIs, but if anyone has a general answer that is suitable for any atlas I will be happy. A step by step guide would be appreciated :) Thanks! -- Sergey ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ROI labels for geometry vertices
Hi Bruce, Thanks a lot! This one does work as described and provides me with information I need. -- Sergey Hi Sergey, here's read_annotation.m. It should also return the embedded colormap that's in the .annot file, including structure names. Not sure why it's not in your distribution. cheers, Bruce ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
