I am trying to run segmentHA pipeline on HCP data. To do so, I have downloaded FS processed-extended structural data, manually made "scripts", "trash", and "stats" folders in each subject's folder [HCP output does not have these folders]. A few notes and questions:

1. segmentHA_T1 runs smoothly. However, I do not know which T1 does segmentHA use, since there are also a few "_hires" (high resolution) files resulting from HCP's structural analysis pipeline (https://github.com/Washington-University/HCPpipelines).

2. segmentHA_T2 also runs smoothly. However, I didn't know which T2 file is the most suitable to be given to this command. I did give T2w_hires.nii.gz (Voxelsize = 0.7 mm isotropic) in the /mri folder of each subject.

3. I statistically checked the correlation between HCP FS generated values of whole hippocampus/amygdala, and segmentHA generated ones. Of note, they were highly correlated (all p-values < 0.001, all r ~ 0.9).

I will be glad to know whether the pipeline I used to analyze HCP data is correct or any further steps are required.

Bests,

Amir