HCP Glasser 360 Atlas: Region extraction in AFNI

AFNI Message Board
1

Dear all,

I would like to extract all regions of the auditory cortex from the HCP Glasser 360 atlas that is already contained in AFNI, that is, from the file “MNI_Glasser_HCP_v1.0.nii.gz” in AFNI’s abin folder. I am refering to all red colored regions in the Figure on the right here: https://balsa.wustl.edu/WN56

In their paper, Glasser et al. included the following regions for the early auditory cortex: “A1, LBelt (Lateral Belt), MBelt (Medial Belt), PBelt (Para-Belt), and the retro-insular cortex (RI)”.

Paradigmatically, the script below extracts the left and right primary auditory cortex.


for roi in L_Primary_Auditory_Cortex R_Primary_Auditory_Cortex
do
3dcalc \
-a MNI_Glasser_HCP_v1.0.nii"<$roi>" \
-expr 'step(a)' \
-prefix Glasser_360_$ROI.nii
done

Now comes my AFNI related question: in the AFNI GUI, I can right click on the brain and select “where am I” to open a new window. This new window then shows me how the regions are really called in the “MNI_Glasser_HCP_v1.0.nii.gz” file, such as " L_Primary_Auditory_Cortex" for the left primary auditory cortex.

But isn’t there an easier way, such as a list, that would show me all regions of the atlas and how they are called in the “MNI_Glasser_HCP_v1.0.nii.gz” file?
I found all regions listed above via “where am I”. My question is really about if there is an easier way to do the same job in the future, e.g., with a different atlas, than manually searching the AFNI coded region names via where am I.

2

Is this what you want:


3dinfo -labeltable MNI_Glasser_HCP_v1.0.nii.gz

or


@MakeLabelTable -labeltable_of_dset MNI_Glasser_HCP_v1.0.nii.gz

?

-pt

3

Thank you, Paul.

This is exactly what I wanted (or needed). Perfect!

Philipp

4

A couple other ways:

by atlas name, instead of dataset file name.

Without -atlas, this shows all atlas indices and labels across all the installed atlases

whereami -atlas MNI_Glasser_HCP_v1.0 -show_atlas_code

show the atlas structure, which is a little different than the labeltable

this contains the center coordinates for each region and long names if they exist

3dinfo -atlas_points ~/abin/MNI_Glasser_HCP_v1.0.nii.gz

5

Thank you Daniel.

This is great info, very useful.