Hi Octavian
Yes, we do usually embed the LUTs into the .annot and .mgz files to make them self-contained. I think Doug has something to read them from at least the .mgz. Maybe mri_info?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Octavian Lie Sent: Friday, January 8, 2021 1:19 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] write .annot files
External Email - Use Caution Thank you, Bruce. Just to exhaust the annot issue. I assume that the labels (parcel names) are not embedded in .annot or aparc+aseg.mgz per se, but they are read from the LUT table by matching annot vertex indices to col 1 in the LUT. Is there any .m file that can do that? If not, I can write one, but wanted to check, thank you. Octavian
On Fri, Jan 8, 2021 at 11:03 AM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Alas there is not – there are large parts of the cortex that have not yet been mapped for microstructural boundaries
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Octavian Lie Sent: Friday, January 8, 2021 11:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] write .annot files
External Email - Use Caution Thank you, Bruce, as always. The BA_exvivo.thresh.annot does not annotate all the vertices, see attached BA.png. Is there a complete Brodmann map like in the atlas image? Thank you, Octavian
On Fri, Jan 8, 2021 at 10:37 AM Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Octavian
1. Yes, there is a write_annotation.m that you can use. 2. We output an annot of the max probability labels at each point I think called BA_exvivo.thresh.annot
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Octavian Lie Sent: Friday, January 8, 2021 11:26 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] write .annot files
External Email - Use Caution Dear All,
These are probably rookie questions. 1. I can read an .annot file with read_annotation.m, is there a way to write one? (for example read it to matlab, modify, and save, or create a combined (lh+rh) aparc.annot file etc.
2. On the same line, how one combines all the Brodmann labels into a Brodmann parcellation, if not done already.. Thank you, Octavian
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