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