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That set of files is too large to be included in some packages.   Not sure what info you are following about pulling the files from GitHub, but for now you could try,

- R.

$ cd $FREESURFER_HOME/python/packages/ERC_bayesian_segmentation
$ sudo wget MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ERC_bayesian_segmentation/atlas_subdirs_20250217.tgz
… wait for download to finish …
$ sudo rm -rf  atlas_full  atlas_simplified
$ sudo tar zxpf ERC_bayesian_segmentation/atlas_subdirs_20250217.tgz
$ sudo rm ERC_bayesian_segmentation/atlas_subdirs_20250217.tgz

On Feb 17, 2025, at 11:27, Chourrout, Matthieu <m.chourrout@ucl.ac.uk> wrote:

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Hi all,

I was trying to run the dev version of FreeSurfer from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ but the content from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://github.com/freesurfer/freesurfer/tree/dev/mri_histo_util/ERC_bayesian_segmentation is not present in ${FREESURFER_HOME}/python/packages/

As instructed, I've put atlas_full/ and atlas_simplified/ inside ${FREESURFER_HOME}/python/packages/ERC_bayesian_segmentation/ when trying to run mri_histo_atlas_segment_fireants but had to manually create the subdir.

can't open file '/share/apps/freesurfer-dev/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py': [Errno 2] No such file or directory

Can the files from ERC_bayesian_segmentation/ in GitHub be manually pulled out into this directory? Which files are required?

Best regards,

Dr Matthieu Chourrout orcid logo 16px
Research Fellow on Correlative X-ray Imaging for the Large-scale Imaging of Neural Circuits
Rm 4.17 Malet Place Eng. Building, Torrington Place, London, WC1E 7JE
Bloomsbury Campus, University College London
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