Re: [brainGraph-help] All atlas in braingraph has even numbers of the areas, and it's effect on the custom atlas.

[Chris Watson]

I think you can set some of them to "B" which means "bilateral" (if I remember correctly; I wrote it a long time ago). So try that.

On Wed, Jan 17, 2024 at 9:16 AM J <june...@empathy-research.org> wrote:

Dear Chris,

I found all the atlas in github has even numbers of the areas.

For several weeks, I struggled with the custom atlas, and found this interesting common ground.

Whenever I try to use the custom atlas with different numbers of areas per hemisphere, or three levels of lobes L, R, and M for brainstem or other 'middle' areas, I get

task 1 failed - "invalid 'length.out' value".

Does the hemisphere and lobes are mandatory for running make_brainGraphList?

Is it impossible to use the function with some 'middle' areas?

Bests,

J.

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[J]

Thank you for the reply. 

I confirmed that it's 'B'.  based on the code.

https://github.com/cwatson/brainGraph/blob/a0d13aea831fbb708c9fb984816e9edda616bbdd/R/import.R#L137

However, Still braingraph can't get the areas maked as 'B'. 

For example, when I (wrongly) change the 'B', to 'R', everything works properly, but 'B' hemisphere with Cerebellum nor Brainstem doesn't work.

While reading the code lines, I guess you might allowed 'B' in very limited usecase (like specific atlas). 

Would you kindly check this, please?

Bests,

J.

[Chris Watson]

In order to debug the issue, you'll have to share your data, the code you ran that resulted in error, and the output of sessionInfo()

Chris

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[J]

I found the solution after several trial-and-error experiemnts : )  the 'B' is used at certain stage, bot the correct one is 'both'. When I put the 'both' for 'hemi' column, the issue resolved.

Sincerely appreciate to your awesome tool, and contribution to open science.