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Dear FreeSurfer-Experts,

I’m in need of your experience to help me with a decision in my current project:

I want to use certain areas, that were identified by structural graph theoretical analyses based on the FreeSurfer parcellation and DTI data, as Regions of interest in SPM. We already have a script that helps with the transfer and creation of ROIs however it is still unclear what’s the best way to create the ROIs. Here are a few of my ideas and pros and cons regarding these:

1. Parcel the MNI T1 standard brain used in SPM with FreeSurfer and create the ROIs from the identified regions from that
PRO: direct use of the standard space, that is later used in SPM’s group level analysis
CON: SPM tends to be peculiar in giving information about their standard template, so I am unsure if the one I found in the spm12-folder is the correct one to use

2. Extract the ROIs of each participant individually and then use SPM to normalize and averaging/summing these
PRO: Ending up in same space as the SPM analysis
CON: identified regions are (at the moment) not individually identified, although they could be; normalization is difficult with just ROIs
ALTERNATIVE: use FreeSurfer not on individual “raw” T1 images but on already normalized T1 images and then do the ROIs individually per participant.

Probably, I am also forgetting another possibility.
I am looking forward to hearing your ideas and comments.
Thank you very much in advance,
Best wishes,
Falko