Please try:

segmentThalamicNuclei.sh   4001   /Applications/freesurfer_dev/freesurfer/subjects/  /Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii    T2_THALAMUS    t2

Cheers,

/Eugenio

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, 8 December 2019 at 15:00
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Thalamic nuclei segmentation

segmentThalamicNuclei.sh 4001 /Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii THALAMUS BBREGISTER_MODE t2