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Hi developers!
I am running connectivity analyses for amygdala subregions using images from a 7T scanner. I am wanting to transform the amygdala segmentations into fMRI space (1.6 iso voxel) for individual analyses and am looking for the best way to do this. Would it make sense to:
1. Inflate the norm.mgz brain, then run the segmentHA_T1.sh script, and then extract the individual segments. 2. Run the segmentHA_T1.sh script as usual, but inflate the rawavg brain. Then, warp the full segmentation to fit the rawavg space (using mri_convert -input <original_amygdala_segment> -at -rt nearest -reference <inflated_rawavg_brain> -output <inflated_amygdala_segment>), and then extract the individual segments.
Does it matter which way I do it? Is there another way to do it that would be better?
Many thanks, Elizabeth