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Hi Eugenio,

I am running this command:
mri_histo_atlas_segment_fireants input.nii.gz out_dir 1 -1 invivo

It fails with the following output:
/hpc/packages/minerva-rocky9/freesurfer/8.1.0/usr/local/freesurfer/8.1.0-1/python/bin/python3: can't open file '/hpc/packages/minerva-rocky9/freesurfer/8.1.0/usr/local/freesurfer/8.1.0-1/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py': [Errno 2] No such file or directory

I am using the stable FS 8.1 release on our HPC which doesn't seem to have the FireANTs scripts. Shall I ask to install the dev version instead?

Thanks,
Francesco

From: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Sent: Tuesday, November 18, 2025 5:02 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: HistoAtlasSegmentation NextBrain with FS 8.1
 
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Dear Francesco,
Can you please send us the command you ran, and the output you got?
Kind regards,
/Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: La Rosa, Francesco <francesco.larosa@mssm.edu>
Date: Tuesday, November 18, 2025 at 10:47 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] HistoAtlasSegmentation NextBrain with FS 8.1

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Good morning,

I have been trying to run the HistoAtlasSegmentation with either FS 8 or FS 8.1. The command fails with both versions as it seems that the FireANTs scripts (eg. segment_fireants.py') are not included in the released code. Could you help me with that?

Thanks,
Francesco