Atlases for timeseries extraction

[FEDERICO CAMPO]

Hi cpac team,

I processed ABIDE I and II dataset with CPAC to extract time series.

I noticed, a lot of altlas are used by default but I didn't find informations about some of them: for example the atlas named: "aal_mask_pad" has some kind of relation with the AAL atlas?

Same goes for "ho_mask_pad" and HarvardOxford atlas.

Where can I find informations about these atlases?

Thanks in advance for your reply

Sincerely

Federico

[FEDERICO CAMPO]

And also, what do Mean-1 and Mean-2 stand for, for each atlas? How can I control this averaging process?

[Jon Clucas, MIS]

Hi Federico,

I noticed, a lot of altlas are used by default but I didn't find informations about some of them: for example the atlas named: "aal_mask_pad" has some kind of relation with the AAL atlas?

Same goes for "ho_mask_pad" and HarvardOxford atlas.

Where can I find informations about these atlases?

Unfortunately, we don't have thorough documentation of all packaged templates. We have an open issue to fill in documentation for the undocumented templates. The packaged atlases come from a variety of sources, which are documented at https://fcp-indi.github.io/docs/latest/glossary/template

And also, what do Mean-1 and Mean-2 stand for, for each atlas? How can I control this averaging process?

 Mean-1 and Mean-2 in what context?

Thanks for raising these questions,

Jon

[FEDERICO CAMPO]

Hi Jon,

Thank you for your willingness, and your help.

I'll try to get as much information as I can from the current documentation.

With Mean-1 and Mean-2 I mean that cpac outputs two timeseries for each atlas: one labeled with mean-1 and the other with mean-2. I link a photo to clarify it.

[Jon Clucas, MIS]

I see, thanks for the clarification!

"Mean" and the integer are separate considerations. "Mean" indicates this output is a result of the Avg analysis for that atlas, and the integer indicates that a fork occurred prior to generating that output (for example, if you ran the default pipeline, you'd have different outputs for after each of the two included regressors ('default' & 'defaultNoGSR')). If you compare the JSON sidecar files, you should be able to see which integer corresponds to which fork.

Avg, Voxel and SpatialReg are the available analyses for timeseries extraction.

[FEDERICO CAMPO]

Hi John Cluas,

Thank you so much for your explanation. Now it’s all more clear to me.

Kind regards,

Federico Campo