Oooohhhh I see. Yeah you’ll have to run in CPU mode on a machine with quite a lot of RAM 😊
-- Juan Eugenio Iglesias http://www.jeiglesias.com From: Keenlyside, Andrew <andrew.keenlyside...@ucl.ac.uk> Date: Wednesday, May 14, 2025 at 3:27 AM To: Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? External Email - Use Caution Dear Juan, This was run with the fast version of NextBrain using the CPU running on a 313um HiP-CT scan of the brain (29MB). The GPU version at this resolution failed when I was trying to run it on a fairly large workstation (A1000 GPU ~48GB VRAM) The issue is not quite the performance of the model at ~300um, we have issues with the running of a 150um scan which is killed during the fitting step. We were wondering which versions you used to get the 150um segmentation of the edlow et al. MRI brain? And if you have any advice which might help us here, Kind regards, Andrew Andrew Keenlyside PhD Student, UCL Mech. Eng. ________________________________ From: Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu> Sent: 14 May 2025 07:25 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Cc: Keenlyside, Andrew <andrew.keenlyside...@ucl.ac.uk> Subject: Re: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? ⚠ Caution: External sender Dear Matthieu, Which version did you use? The FireANTs version, I presume? Can you please share some screenshots of the incorrect registration? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Chourrout, Matthieu <m.chourr...@ucl.ac.uk> Date: Tuesday, May 13, 2025 at 6:17 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Cc: Keenlyside, Andrew <andrew.keenlyside...@ucl.ac.uk> Subject: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain? External Email - Use Caution Hi Freesurfer Community, The NextBrain page showcases the results of the pipeline on the Edlow brain binned at 200um, but we weren't able to reproduce this on our data with a voxel size < 300 um (thus we binned the data). With my colleague Andrew, we've pinpointed the issue to the cartoon fitting step. On what system was the NextBrain run at this resolution? I assume it was run on CPU only? Did you have to tweak the cartoon or other key steps to make it run? 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