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

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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.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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Octavian Lie
Sent: Friday, January 8, 2021 11:59 AM
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Subject: Re: [Freesurfer] write .annot files

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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.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.edu <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.edu>
Subject: [Freesurfer] write .annot files

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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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