extracting hippocampus from freesurfer parcellations on BATMAN tutorial

1

Hello mrtrix3 experts,

I am a new user.

I am trying to extract the hippocampus from the sample T1 provided by the batman tutorial. I’m using FreeSurfer’s mri_extract_label command on the file hcpmmp1_parcels_coreg.mgz to extract ID 366 which corresponds to the L_Hippocampus per the hcpmmp1_ordered txt file.

The command I’m using is mri_extract_label hcpmmp1_parcels_coreg.mgz 366 left_hippocampus.nii.gz. The hcpmmp1_parcels_coreg.mgz (after converting from .mif) is straight from the supplementary file, I didn’t generate it.

The issue is that when I load left_hippocampus.nii.gz onto my T1_coreg.mif file on mrview, it highlights the entire brainstem instead of the hippocampus. I’ve done similar commands for motor cortex, thalamus, and cerebellum which all appear where they need to be anatomically-speaking…

I’d appreciate any help!

2

Hi Huy,
The following might work:

for index in 366 375
do
mrcalc hcpmmp1_parcels_coreg.mgz $index -eq ROI_${index}.mif.gz
done

It might be worth checking the index of the region(s) of interest in hcpmmp1_parcels_coreg.mgz

Hope this helps :slight_smile: