Hello,
I am hoping to gray matter mask my fMRI data at the individual subject level to be more consistent with analyses collaborators are using in other imaging softwares. Presently, we use afni_proc.py to preprocess data without any masking, 3dDeconvolve for individual subject GLMs, and 3dLME for group level analyses, in which we apply a whole brain mask. It's not immediately clear to me at which stage it would make the most sense to implement the mask. I've been reading the help pages and have come across some gray matter segmentation commands for afni_proc.py, but I'm not sure how this would affect blurring (currently using FWHM of 6 mm) and which outputs would be relevant for later stages of analysis. Would it be advisable/not advisable to preprocess data as normal and then apply the gray matter mask in the GLM stage?
Thank you for your time!
Edited 1 time(s). Last edit at 05/27/2015 03:57PM by alibc90.
