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 <bfis...@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@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.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 <bfis...@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@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 > > > > * 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1GClafP66RK9v8_-_0934OEdqk6RJdYujTJwL3JvppSxrEeySzz1ZUWDurcKLm9W3HiLc0bnmiRx__NV4OufHeXVpeoq4RZppxeX59MnlYWNDWYGsz1nlkER99NENsaCRc1ZZa3wfvm-PX_seCHMP5H6PVhkeFRQFXZvFU1cDGU1A2W3t06oCD9ovIXc8ndYQcRiw8xp1beJBqcB-iuya36umIf5bEEYIseH5o1o4vTl7jpeG5x9hjP8Z_9rKoFiDLBaReR5b2bbik7XaxI-hVA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/1P4daN2GG21ElzSGKBohZlaIIRLvcqrrR66eyxBX6lXOCkUmHrPAvFuYWTh8ezaaTNbqPIL35vSAJY2HACOCFJuzLqdIwbiQqVnJOlrfH9OI69Trj-Pu4P_tbBGRgz7OrX8v6Niyh8lB5v60k8DgsV719wkJ23I7Mm8oujFrQWKOGIVIuekzkUD_UMzlgK4lEkgeDXGe24Im0SiZ3cjdhI1bvNwubmj40cchvBJwAin4TSNlFkYr1sCQaylRbwm8ud70ake4I28qgN9SfRE-mcw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1GClafP66RK9v8_-_0934OEdqk6RJdYujTJwL3JvppSxrEeySzz1ZUWDurcKLm9W3HiLc0bnmiRx__NV4OufHeXVpeoq4RZppxeX59MnlYWNDWYGsz1nlkER99NENsaCRc1ZZa3wfvm-PX_seCHMP5H6PVhkeFRQFXZvFU1cDGU1A2W3t06oCD9ovIXc8ndYQcRiw8xp1beJBqcB-iuya36umIf5bEEYIseH5o1o4vTl7jpeG5x9hjP8Z_9rKoFiDLBaReR5b2bbik7XaxI-hVA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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