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______________________ Shasha Li MD, PhD Assistant Professor, Martinos Center/Radiology (She/her/hers)
Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 T 617-642-0449 massgeneral.org
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: Thursday, February 29, 2024 5:00:01 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 240, Issue 19
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Today's Topics:
1. Re: Support Request NextBrain (Sorby-Adams, Annabel) 2. Re: Longitudinal Freesurfer in the presence of large tissue defects (Philip P) 3. mri_synthseg fails with current model files (was Re: Support Request NextBrain) (fsbuild) 4. Re: [ext] Re: mris_convert reading surf.gii files? (Westin, Karin) 5. Re: [ext] Re: mris_convert reading surf.gii files? (Huang, Yujing) 6. Re: [ext] Re: mris_convert reading surf.gii files? (Westin, Karin) 7. Re: Creating a custom registration template with FreeSurfer template (Huang, Yujing) 8. Re: [ext] Re: mris_convert reading surf.gii files? (Huang, Yujing) 9. Re: [ext] Re: mris_convert reading surf.gii files? (Westin, Karin) 10. Re: [ext] Re: mris_convert reading surf.gii files? (Huang, Yujing)
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Message: 1 Date: Thu, 29 Feb 2024 01:11:25 +0000 From: "Sorby-Adams, Annabel" ASORBY-ADAMS@mgh.harvard.edu Subject: Re: [Freesurfer] Support Request NextBrain To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: fsbuild fsbuild@contbay.com Message-ID: CF02DF80-4A65-4780-85A0-26F4D30B59B4@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi Helen,
I managed to run mri_synthseg on my M2 Mac by coping over the model file to the 7.3.2 version of freesurfer, and installing the tensorflow workaround previously posted on the forum for apple silicon machines.
I have not been able to get it to work on the 7.4 or most recent dev versions unfortunately. The work around for 7.3.2 isn?t ideal, but does the trick.
Freesurfer gurus may have more insight though! Annabel
On 28 Feb 2024, at 20:03, Friedrich, Helen hfriedrich@bwh.harvard.edu wrote:
? Hi R,
Thanks for your quick response.
We actually did that initially and it did not work unfortunately.
Could you provide me with segmentations for a certain scan? Or do you see any other possibility to make it work?
Best,
Helen
______________________
Helen Friedrich, B.Sc.
Doctoral Student
Netstim Laboratory
Center for Brain Circuit Therapeutics
Department of Neurology
Harvard Medical School
Brigham and Women?s Hospital
75 Francis St, Boston MA 02115
brighamandwomens.org
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________________________________ Von: fsbuild fsbuild@contbay.com Gesendet: Mittwoch, 28. Februar 2024 17:20 An: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Friedrich, Helen hfriedrich@bwh.harvard.edu Betreff: Re: [Freesurfer] Support Request NextBrain
External Email - Use Caution
The mri_synthseg script and python in the freesurfer disrtibution you are running are not entirely compatible with the arm64 M1, M2, M3 processors in silicon Macs. You could try installing and running the development build of Freesurfer for the silicon Mac via the link below. (After download, right click on the .pkg installer, and select open with default, then follow the prompts).
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-...
We would be interested to know if you run into such issues with the above development build. Please keep in mind a development build can be unstable and has not been tested like an actual release. Your numerical result may differ with the development build compared to the previous build/release.
- R.
On Feb 28, 2024, at 14:25, Friedrich, Helen hfriedrich@bwh.harvard.edu wrote:
Dear Support Team,
I'm reaching out for assistance with setting up NextBrain - mri_synthseg.
Unfortunately, I could not make it work. There seems to be an issue with the np.float128-section. This error keeps showing up: <image.png> I have also tried to delete np.float128 from the script (as per suggestion from my colleague). However, the same error showed up.
I'm working on a macOS M1.
I would be very grateful for your assistance.
Best,
Helen ______________________ Helen Friedrich, B.Sc.
Doctoral Student Netstim Laboratory Center for Brain Circuit Therapeutics Department of Neurology Harvard Medical School
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