display atlas with very many areas

AFNI Message Board
1

I remember seeing a trick to make AFNI GUI display an atlas with very many areas and (like rhesus monkey ARM, where index numbers go up to 1825) with truly unique colors... without the trick the adjacent areas sometimes show in the same color.

Can you point me to the instructions how to do it? I can't find those.

Incidentally, has ARM been published? I can only find references for NMT (Seidlitz 2018), CHARM (Jung 2021) and SARM (Hartig 2021)

2

Hi, Pawel-

To open AFNI with up to 2048 colors:

afni -XXXnpane 2048

... and then you can select "ROI_glasbey_2048" as the colorbar.

--pt

3

... and now seeing your second question about ARM, I think it is out, but will let @dglen provide a real answer.

--pt

4

Thanks! Is there an environmental variable or some other way to to make -XXXnpane 2048 permanent?

My AFNI usage scenario is months of use separated by months of doing something else and I am afraid I might be back next year with the same question :fearful:

5

Sorry to hear your run-ins with AFNI are so sparse.

Fortunately there is a machine learning algorithm that suggests previous questions/threads if you ask something that had been asked before.

Also, you could make an alias, for example in bash:

alias afni='afni -XXXnpane 2048'

--pt

6

Oh, and actually you can also have AFNI save the way you open+view data in a layout file, see this AFNI_LAYOUT_FILE env var here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/afniandafni/readme_env_vars.html

--pt

7

Yes, the ARM (combination of CHARM+SARM atlases) should be there with @Install_NMT. Let us know if you're not seeing this.

8

Thank you, Paul! I tried an alias but it did not work for me for a reason so stupid that I am embarrassed to tell. Now it works great, together with my previous startup option that I was setting with an alias, that is xhair gap size. AFNI_LAYOUT_FILE is very helpful, too!

Daniel: I have ARM but I was asking if there is a published paper about it.

9

No, there was no publication for the simple combination. I will add the CHARM atlases are based upon Saleem's D99 atlas, so if you are using ARM, you should cite the 3 papers (Jung (2021), Hartig (2021), Reveley (2017)). There is also the update to the D99 atlas that includes subcortical regions (Saleem 2021).

10

Thanks!

Pawel