Parcellation of a network (TT_Daemon TLRC space)

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Hello folks,

I am not sure if it is a relevant question, but if someone can give me a clue, I’ll be able to carry on in my study.

I am reading several publications that refer to cognitive control network, or default mode network.
I would like to isolate these areas (parcellation) after afni preprocessing and regression (I’m in tlrc space).

The trouble is I don’t have much anatomical knowledge, and have trouble finding the correspondance between the areas named in the different publications (that differ from one publication to the other), and the areas in the atlases (TT_Daemon in occurence, Talairach space).

Are there network atlases that we can use in AFNI ?
Or would you have a website that could enlight me on the different names/parcellations of the different networks/areas of the brain ?

Thanks for any help

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Hi-

You can use any atlas or template that you want when using AFNI. We provide several, for spaces.

It is true that the different names of regions in different atlases—sometimes due to the different origins of the region, such as functional, anatomical, cytoarchitectural, etc.—is confusing.

These are the atlases and templates we distribute in the standard binary package download:
https://afni.nimh.nih.gov/pub/dist/atlases/afni_atlases_dist/
… and a list of “other” templates and atlases we distribute are here.
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/template_atlas/other_tas.html
… and you can also use any other valid datasets you want.

Note that the atlases/templates we distribute have labeltables in them, so you can see the names of regions when using the AFNI GUI, particularly with the whereami feature, and with the command line program whereami. More about this specifically is addressed here:

–pt

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Hello P.T. thanks for your reply.

I forgot to mention, but I work remotely, so in bash command line.
It doesn’t change much as I can still view atlases with mricron locally, but I don’t have afni on my connection computer.

This is very nice resources links you provided. I am sure I will find the good atlas I need.

Regarding the comprehension of the labels, is there somewhere where the names are explained ?
for instance : ctx_lh_G_and_S_paracentral. It is rather difficult for a neophyte to understand. Is there a ditionary somewhere ?

One last question, if my coregistration is done in TLRC space, shall I only use TT atlases or does any +tlrc atlas work (I know +tlrc is a convention name for any coregistered volume, but maybe atlases names differ) ?

Thanks

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Don’t have AFNI on the local machine — eek! Well, no worries, but if you do change your mind, there are install instructions available for most OSs:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/index.html

Indeed, the ROI names are abbreviations that require unpacking (and many can be quite cryptic).

In general, I think you have to back to each original source, which might have a paper that describes the regions, or even more hopefully a supplementary spreadsheet describing them.

For FreeSurfer ROIs, which seems to be the one listed here, they are labelling according to 2 atlases: The Desikan-Killiany, and the Destrieux. From here:
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
… they link to the papers under “Atlases”, and they also link to this:

form more descriptions.

Apparently, Slicer has some further tabular description of them:
https://www.slicer.org/w/index.php/Slicer3:Freesurfer_labels

Re. TLRC-ness: Indeed, the +tlrc suffix in AFNI is essentially generic for “dataset is in a standard space”, which might specifically be Talairach-Tournoux, MNI, India Brain Template, Haskins Pediatric Template, or more… You should always pair a particular atlas to the particular template space. So, you would not want to put the Glasser atlas (defined in MNI space) directly onto the Haskins Pediatric template without a nonlinear transform/mapping/warp of it. You should always view the atlas over the template to make sure it seems sensical.

Note that there are maaaany variations of some spaces as well, such as of the MNI (symmetric and asymmetric; different creation methods; different generations; different centering), so be as specific as possible in your pairing.

–pt