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Hi Eugenio,

Thanks for the quick reply. I’ve tried two versions of FreeSurfer—7.4.1 and 8.1.0— on Ubuntu 22.04.5 LTS (64 bit GNOME version = 42.9) but both failed with the following error message: “using 1 thread predicting 1/1 Killed”.

Any idea how to fix it?

I’ve copied the sample data ‘bert’ into my home directory and ran the following commands in the terminal:

export FREESURFER_HOME=/usr/local/freesurfer/8.1.0

export SUBJECTS_DIR=/home/juen

source ${FREESURFER_HOME}/SetUpFreeSurfer.sh

mri_segment_hypothalamic_subunits --s bert

Here are the output in the terminal:

-------- freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed --------

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME /usr/local/freesurfer/8.1.0

FSFAST_HOME /usr/local/freesurfer/8.1.0/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR /home/juen

MNI_DIR /usr/local/freesurfer/8.1.0/mni

using 1 thread

predicting 1/1

Killed

best,

Juen

On Fri, Aug 1, 2025 at 4:25 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Dear Juen, I just checked and mri_segment_hypothalamic_subunits is part of 7.4.1. Can you please double check? If it isn’t there: what OS & exact version are you using? Cheers, /Eugenio

--

Juan Eugenio Iglesias

http://secure-web.cisco.com/1mVUny65G1SqnJNMgQ_WWmKT-8SZkTs1Sy6n2oxK6lfbmVVT... *From: *Juen Guo juenguo@gmail.com *Date: *Friday, August 1, 2025 at 10:59 AM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Segmentation of the Hypothalamus in FreeSurfer 7.4.1

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Dear FreeSurfer Expert,

I am trying to segment the subunits of the hypothalamus using FreeSurfer 7.4.1, but the segment_subregions command does not include an option for the hypothalamus in this version. I found that version 7.2.0 includes the command mri_segment_hypothalamic_subunits, but this command is not executable in version 7.4.1.

My questions are:

1. Do I have to downgrade to 7.2.0 to use this function?
2. Why was this function discontinued in version 7.4? Was it removed

due to defects or other issues? 3. Is there any alternative way to segment the hypothalamus in FreeSurfer 7.4.1?

Best, Juen _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu

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Hi Douglas, Yes, the file mri_segment_hypothalamic_subunits is present in version 7.4.1. However, it gives an error message — 'using 1 thread predicting 1/1 Killed' — when I run it. I even tried copying the file from version 7.2.0 to the 7.4.1 folder, but it still doesn't work. The only viable option might be to keep both versions of FreeSurfer installed concurrently. Best, Juen

On Sun, Aug 3, 2025 at 6:50 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

hmmm, it appears in my version of 7.4.1. Are you sure it is not there? If not, then you can just copy it from 7.2 to 7.4.1

On 8/1/2025 10:58 AM, Juen Guo wrote:

    External Email - Use Caution

Dear FreeSurfer Expert,

I am trying to segment the subunits of the hypothalamus using FreeSurfer 7.4.1, but the segment_subregions command does not include an option for the hypothalamus in this version. I found that version 7.2.0 includes the command mri_segment_hypothalamic_subunits, but this command is not executable in version 7.4.1.

My questions are:

1. Do I have to downgrade to 7.2.0 to use this function?
2. Why was this function discontinued in version 7.4? Was it removed

due to defects or other issues? 3. Is there any alternative way to segment the hypothalamus in FreeSurfer 7.4.1?

Best,

Juen

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