Thalamic atlas shifted

Bugs
1

Hi, Brainstorm team,

I am projecting a thalamic volume called 'ThalamicNulcei.v12.T1.mgz'.
However, I have difficulty that some patients have shifts compared to the T1 MRI.
Following is how I am importing files.

  1. Right click subject -> import MRI (volume atlas (subject space)) -> import ThalamicNulcei.v12.T1.mgz'
  2. MRI orientation: yes -> SPM/MNI: Ignore -> reslice :yes

The thalamic atlas is shifted toward lower in several subjects.
This does not happen if I see it in a freeview.

Screen Shot 2024-07-09 at 9.59.18 AM
Screen Shot 2024-07-09 at 9.59.18 AM1684×1380 253 KB

Is there a way to fix this?

Thank you very much for your help!

1 Like
2

Hi Aida!
Don't you want to share this atlas file with us (BS community)? :face_with_hand_over_mouth: :clap: :pray:

Thanks in advance :smiley:

3

Hi tourette,

Sorry, I can't share it; however, I came up with a solution.
When importing Apply that standard normation : No -> Transormation in the MRI file :yes -> SPM/MNI: Ignore ->reslice :yes.

This fixed the location.
Hope this make sense.

Best,

1 Like