Dear Amir,

The scripts are certainly there:

https://github.com/freesurfer/freesurfer/tree/dev/mri_histo_util/ERC_bayesian_segmentation/scripts

Maybe it’s easier just to install the development version of FreeSurfer?

Cheers,

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh <amirhussein.a@gmail.com>
Date: Monday, January 20, 2025 at 5:56 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] NextBrain: no segment_fast or segment_fireants.py

External Email - Use Caution

Hi Freesurfer users/experts,

I was trying to run NextBrain (cloned from here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/freesurfer/freesurfer/tree/dev/mri_histo_util), and asked HPC admin to install atlas_full and atlas_simplified in the designated folders, but encountered this error that segment_fast.py is not available in FS_HOME/python/packages/ERC_bayesian_segmentation/scripts/segment_fast.py (or segment_fireants.py).

The code I run (in the folder of the downloaded tool):

./mri_histo_atlas_segment_fireants /path/to/input/T1.nii.gz /path/to/output/folder 0 dct

I'm using FreeSurfer 7.4.1.

Any help would be appreciated.

Best,

Amir