Dear Alfonso / CONN community,

I would like to use subject-specific ROIs for certain 'sensitive/small' areas in the MTL (hipp. subfields, entorhinal c.)
Up to now I have done a first analysis using the data at the MNI-space.

I imported directly/manually via conn batch the MNI-space preprocessed images (preproc was done at fMRIPrep).

I saw in other posts that I could add via batch the raw fMRI in addition to the preproc data I have already imported & specify to CONN to do things separately for some ROIs on native-space and the rest keep them at MNI-space.
But it is unclear to me how to do this. 

In a previous thread:
https://www.nitrc.org/forum/message.php?... 
You mention: 
"...(if your functional volumes defined in batch.Setup.functionals are in MNI space and are named 'swauFunctionals.nii', for example, this rule will consider instead the files named 'auFunctionals.nii' -in subject-space- when CONN needs to extract BOLD-signals from your ROIs; see help conn_batch for more details)"

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Can you elaborate on what you mention with "swau" and "au"?
how I could deal with that in my case using the batch? (fMRIprep preproc data manually imported via batch)

2) does it make sense later to use the subject-specific ROIs (e.g. entorhinal c.) to see connectivity with other mni-space ROIS? (MNI-space ROIs default from CONN) e.g. FPN.lateral PFC

Would that work well with CONN ? What would you recommend?


Thank you very much for the help :)