Re: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain?
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.23@ucl.ac.uk Date: Wednesday, May 14, 2025 at 3:27 AM To: Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@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?
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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. JIGLESIASGONZALEZ@mgh.harvard.edu Sent: 14 May 2025 07:25 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Keenlyside, Andrew andrew.keenlyside.23@ucl.ac.uk Subject: Re: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain?
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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
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Chourrout, Matthieu m.chourrout@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.23@ucl.ac.uk Subject: [Freesurfer] Run NextBrain on a high-res 3D dataset: tweaks required for 200um on Edlow brain?
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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?
Best regards,
Dr Matthieu Chourrout [Image removed by sender. orcid logo 16px] https://secure-web.cisco.com/1tiMIHDVZbi1_soxzRzk-v66TQ9fs4j0sOPE5nQKOghqmPCbTrhwSaTPfpnxSdARQKbAEQje-REikDuSM16D6HxBsA1I5iTrncEToD4dYzCbGaQ1h6sLrEAe2JH5qGXVFRPTt0Rsrd0GzjSq6OeKZFbx1Mnk6uDnWSQceO2u4Y3nzsoHJGXDVR_swYlewjBAXZ4LRIyQc_MaYR-15E4BOUxHNvWNsKdpWwEz8n4jrstyvGF9vsHwoey9gJql5IQ01-m7GqtoeE4wuXQW--2-akFIN9h3wUzXjOWMfFADRIcAINOllz5_uhx7DsoUGFlk_MFu0D1ooJA8gDP7YHT95V93iNVoq3S0dWOyfyaagjyI/https%3A%2F%2Forcid.org%2F0000-0002-2282-6976
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Iglesias Gonzalez, Juan E.