AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Renzo Huber
July 05, 2018 11:00AM
Hi Sarah,

Yes, there are multiple approaches on how to get estimates of cortical depths with AFNI tools.
E.g. identifying voxels of a given cortical depth with 3dSurf2Vol using Freesurfer GM and WM surfaces as input. Note the arguments –f_p1_fr and -f_pn_fr that defines the range of cortical depth.

See a full example here: https://layerfmri.com/2017/11/26/getting-layers-in-epi-space/ (go to point 4.) )

Daniel Glen also developed a set of new tools on estimations of cortical thickness that can be used to obtained estimates of cortical depths referred to in his HBM poster (https://ww5.aievolution.com/hbm1801/index.cfm?do=abs.viewAbs&abs=1326) and here: https://layerfmri.com/2018/01/04/layer-fmri-software-in-the-field/#AFNI. Maybe they are of interest too?

Best regards,
Renzo
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Approaches to subdivide cortical layers

SarahChang July 04, 2018 11:45AM

Re: Approaches to subdivide cortical layers

Renzo Huber July 05, 2018 11:00AM