I'm not sure what you mean by "inflate" here. Do you just mean to run recon-all? Usually, you would run recon-all, then run segmentHA, then register the fMRI to the anatomical (bbregister), then map the segs to the fMRI space (mri_label2vol), then run something like mri_segstats --seg segs-in-fmri.mgz --ctab ctab-for-HA --excludeid 0 --avgwf ha-avgwf.dat --i fMRI.nii.gz the ha-avgwf.dat will have a column for each seg in the ctab (excluding 0)

On 8/21/2022 9:57 PM, Elizabeth Haris wrote:

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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

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