Approaches to subdivide cortical layers

AFNI Message Board
1

Hi All,

I’m wonder if there are some approaches that could subdivide cortical layers according to its cortical depth (e.g. depth based on the interface between grey matter and white matter). For example, I have a high-resolution anatomical image and a V2 mask, I’m going to separate V2 into superficial, middle and deep layers. Would it be possible to do this kind of analysis with AFNI?

Many thanks,
Sarah

2

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[/url]) and here: [url=https://layerfmri.com/2018/01/04/layer-fmri-software-in-the-field/#AFNI]https://layerfmri.com/2018/01/04/layer-fmri-software-in-the-field/#AFNI. Maybe they are of interest too?

Best regards,
Renzo