On Aug 19, 2020, at 10:18 PM, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Dear HW,

What was the exact command you ran?

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 Haewon Roh <rofree1st@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, August 19, 2020 at 03:26
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] " quantifyThalamicNuclei.sh" commend does not work..

 

        External Email - Use Caution        

Hi team. 

 

I'd like to collect all kinds of volumes of subjects' thalamic nuclei but

the command " quantifyThalamicNuclei.sh"  does not work in my mac book's terminal window. 

 

(there's no error message but any file was not made after that command ; please find attached screenshot showing the this problem)

 

Before doing that command on terminal window, I made sure that every subject file had three files (ThalamicNuclei.v12.T1.FSvoxelSpace.mgz, ThalamicNuclei.v12.T1.mgz, ThalamicNuclei.v12.T1.volumes) after the process of segmenting thalamus.

 

 

 

But, for hippocampal and amygdala subsegmentations, command of "quantifyHAsubregions.sh" is working well.. 

 

What is the difference between thalamic nuclei and hippoamygdala substructures for gathering all volumes into tabelfile ?

 

my subjects were preprocessed with freesurfer version 6.0 and their substructure segmentations were made using freesurfer version 7.1. Does this make this problem?

 

I attached screenshot of my terminal window as below..

 

Thank you always !!

-- 

Hae Won ROH, M.D.

H.P: +82-10-4341-8142

E-mail: rofree1st@gmail.com

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