Dear Zhac,

Apologies for the mistake in the wiki. As explained in the error message, the subjects directory is the second argument. Also, if you are using a T2 scan, I would replace t1 by t2 in the last argument.

The call should be:

(For a T1 additional scan)

segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/ /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t1

(For a T2 additional scan)

segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/ /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t2

Cheers,

/Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London, and

Research Affiliate

Computer Science and Artificial Intelligence Laboratory (CSAIL)

Massachusetts Institute of Technology

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of zhac looch <Z30D@hotmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 23 November 2018 at 16:32
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] thalamic nuclei additional scan error

External Email - Use Caution

Hi Freesurfer Team,

I want to add additional scan my thalamic segmentation. but my code is not working. where is the error in my code?

thanks for help

my code:

segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t1

my error:

Usage:

segmentThalamicNuclei.sh SUBJECT_ID [SUBJECT_DIR] [ADDITIONAL_VOL ANALYSIS_ID BBREGISTER_MODE]

Or, for help

segmentThalamicNuclei.sh --help