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, /E
-- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh <amirhussei...@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<https://secure-web.cisco.com/1UpUf_-L1H1hsaTNLobhBBGoHrKNtCqL7zDwyidsUOHZH8smH10XJiBnxtCbpKN33hNCybEMSSKYo-nCdaX6WUDTdixv-K0w3Hay60KZ6qyp76TSe7MS0J16_cbYJ-lfOTsW9UYMnB7vFGkCxBebkx56VhM5k4vbsliMR5r83Wof0CFH5S--kF7SRX2h8CkWCrvXt17MsRjq3OIpspflrbBHvq7nQzcsII90ifhrfeDF6g9UM6PZ8KyaqnVGQ3hQW6YTpXyzSWsJbPGgq1-BODXIkRcTcANTq2CFaqHGvalOQRiWgZON3c9t4JfWFOFFEstPGKImnj6gcui1mIbbLEQ/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Ftree%2Fdev%2Fmri_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
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