Weird! Did you try providing the subject directory explicitly as third argument?

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: Haewon Roh rofree1st@gmail.com Date: Wednesday, August 19, 2020 at 09:21 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu Subject: Re: [Freesurfer] " quantifyThalamicNuclei.sh" commend does not work..

External Email - Use Caution Cause I segmented thalamus using only T1 image, I put the this command : quantifyThalamicNuclei.sh thalamus_nuclei_output_file.txt T1 But any file was not made after this command.

On Aug 19, 2020, at 10:18 PM, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto: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.comhttp://www.jeiglesias.com/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Haewon Roh <rofree1st@gmail.commailto:rofree1st@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, August 19, 2020 at 03:26 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: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.

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