Umm it’s weird that it’s looking inside /hpc/packages/minerva-rocky9/freesurfer/8.1.0/usr/local/freesurfer/8.1.0-1/python/packages/ERC_bayesian_segmentation//scripts/ instead of /hpc/packages/minerva-rocky9/freesurfer/8.1.0/python/packages/ERC_bayesian_segmentation//scripts/ Is FreeSurfer being sourced correctly?

Either way: I’d recommend installing dev for the latest version ;-)

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: La Rosa, Francesco francesco.larosa@mssm.edu Date: Tuesday, November 18, 2025 at 5:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: HistoAtlasSegmentation NextBrain with FS 8.1

External Email - Use Caution 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

USE CAUTION: External Message. 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.comhttps://secure-web.cisco.com/1PYJIIt1fXH5qvA0wGrv2_-SgKqKVf7FEGcv_-CaA0k5GDcOpXlzAtu4-ibaQP2q8mRu9W_jPAmEKe4aSXL9fV_If00USMzDsIOX7sDBe7bOL9_YBwVtAlwUymBXeF7Rk7HXX7WApNv2b_8hp9l6L8mpM_UImGZhuZvW7HvDU-YaZjmqxucJuMdYleOKRd1D5zucGFpBuxbDyhT_Ar0ulysjL9VHpdHMfDBSMMH7Rw_aCbfKi9vdEnwgGeCwEZygMNpE3PYHW8S-vB2BXnIooTnZo6r2vU6eMc5kmgBfipOGbGr8lGpjUIUFCfutz2-RR7IIKUCRq3PbHVgM7yRVi9QD3kgYnUrqBwnu2v3vHzkc/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.jeiglesias.com%26d%3DDwQGaQ%26c%3DshNJtf5dKgNcPZ6Yh64b-ALLUrcfR-4CCQkZVKC8w3o%26r%3DUp25rdnho9tD5XG5lQ5eejQBkxSkOcdRL3RMUymffZE%26m%3DHjcGSAAQvdj5u87aT_CXUqxQlM0P-5rw_7udj49DCsExc2eSJVzxzQogi0Gr19Bi%26s%3DvW0tiKmg0cfhnxvwjkoO1gcSzUk2HdOHX_P0-D-g8xE%26e%3D

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

External Email - Use Caution Good morning,

I have been trying to run the HistoAtlasSegmentationhttps://secure-web.cisco.com/1kSjSiwmOkXuV9ZohbkqAAu5Ha-SlDWW2oN9VbMJZGnpK_dsU8VG0-dP5U0m3Qi6wry8tdKkrp0CyJv6Wm3-rt1zqTxraIEUhuEgYo4evCrrY91Zc53QCs6JOdcc4cpxL0OYLMvv6xeh4RLr4f8Jek6Z3WJiBm-5SX7e4Kvty4xM5itjYTTHnmYIqarRdmNxFT5YbiS0s49S5nS_vy0o9vHNuFKHxIxwJi9YFij_tIrjXbOScWRdQYR_TuXoiC54AxI5klsHc1EBaH7y7ayQQqwxqGTyw5Z-PriupgS-y-UJI7lETX40BoJ9CjamyFxMkt9QRXVfm_S29uosroLQhKQSd0rKRq89fCiEs4wKs9JU/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1ZIvtpmNUrrYqX7-5Fh4BlvrEnYVZIRoEE4tdMenRNNTEsEzP-5FA0PANORagmkti3VwccvlRfazoeVYZM0qRNDGfIhC7-2DvazOwgjSr2kwwhM7GpoJy8hANG1nT4NDz95UZYUFmyMGHbfqFEqt51lW-2DtcG1Dc57b6ZE-5Fa05qEkCEPCUB6bj040J6cBeHqjij5JAy4EQF1ssj3pyfbOW6AdSOKQ-5FNoEyHbdFabhNDslfxljiJ9nNXCOjCip18EWUSeQL9r35LM8JW2aHL-2DuJ5ebS5aTGhrXRBzvsgKmy-5FAdUakNciW1fBxWe-5FPnHPzYfv7qAu41qVho5ilQFOjIJB4VQfx3A_https-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FHistoAtlasSegmentation%26d%3DDwMGaQ%26c%3DshNJtf5dKgNcPZ6Yh64b-ALLUrcfR-4CCQkZVKC8w3o%26r%3DUp25rdnho9tD5XG5lQ5eejQBkxSkOcdRL3RMUymffZE%26m%3DHjcGSAAQvdj5u87aT_CXUqxQlM0P-5rw_7udj49DCsExc2eSJVzxzQogi0Gr19Bi%26s%3DHc1vI6vl13quarxEaN1S1DcTKZXYqoPJqYRtPjbLXn4%26e%3D with either FS 8 or FS 8.1. The command fails with both versions as it seems that the FireANTs scripts (eg. segment_fireants.pyhttps://secure-web.cisco.com/1mB26ea8LAKatlJdSS62tj7Bk8-I7agMhGNJkgNwG2f9JdYOpDvEvg-NOFL-DEc9_5zcdSv0-cdjeAprf_q8bVSEjSAlb1mwMatLwvoWuOhRxZSJhZwxykxpxnnLf0risgYy1okaEV6qlL8yNdak0VcPqY8zjVYo04CE8j6rg9VzFJCwagfWQjO4qUd3BgUkH6ZUi4yeXZT2ziTbl-GuLB8Q1b0NhWSDHyW4OBfvqiJ-hHRmyDQ15B9tTPKMRx1uzCdlyb0g4iymZ_NaKbh7vhlSVWX1L0mFxW6zm_9CdewoZBzFXiFIJmPUM-H-gVqOeB9LSDDmVSvNnpLZYxxwYBD9P8XPga4tRURgw9zwitiw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__segment-5Ffireants.py%26d%3DDwQGaQ%26c%3DshNJtf5dKgNcPZ6Yh64b-ALLUrcfR-4CCQkZVKC8w3o%26r%3DUp25rdnho9tD5XG5lQ5eejQBkxSkOcdRL3RMUymffZE%26m%3DHjcGSAAQvdj5u87aT_CXUqxQlM0P-5rw_7udj49DCsExc2eSJVzxzQogi0Gr19Bi%26s%3DPkstn-LbyfNAIz-DeoxfRGv3zYlbfd509U1fyF9qGWo%26e%3D') are not included in the released code. Could you help me with that?

Thanks, Francesco