I have found that mri_synthseg v. 7.4.0 in WSL is finicky even with 32 Gb RAM. It seems to work most of the time with 32 Gb RAM by using .wslconfig to limit WSL physical memory usage to 24 Gb and swap at 32 Gb. (synthseg uses about 1-2 Gb of swap in this scenario). The problem is that Windows takes 6-8 Gb RAM so even if you have 32 Gb RAM it still needs to use swap. And it did not work with 16 Gb physical memory even with high swap sizes.

Here is the .wslconfig I used:

[wsl2]
# Limits VM memory to use no more than x GB, this can be set as whole numbers using GB or MB
memory=24GB
# Sets amount of swap storage space
swap=32GB # 32 is probably much more than necessary
# Sets swapfile path location, default is %USERPROFILE%\AppData\Local\Temp\swap.vhdx
swapfile=P:\\Users\\Username\\WSL\\wsl-swap.vhdx # sometime the swap file gets corrupted so it is good to know where it is to delete it
kernelCommandLine = "vm.overcommit_memory=2" # not sure if this is needed

On Thu, Dec 21, 2023 at 9:48 AM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Dear Chuyue,

It’s very posible that you ran out of RAM. I think you need about 32GB to run this module. Do you think that could be the problem?

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 赵楚越 <zhaochuyue21@mails.ucas.ac.cn>
Date: Thursday, December 21, 2023 at 04:17
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Killed procees during running WMH-SynthSeg

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Dear freesurfer experts,

I have installed the develpment version of FreeSurfer on WSL with UNbuntu 20.04, when I try to run WMH-SynthSeg with mri_WMHsynthseg --i WMHsynthsegTset/ --o WMHsynthsegTset/ but the proceess seemed killed and nothing produced in the output directory. Would you recommend what I should change? Thank you so much! Following is the ouput in the commomand line window.

Arguments seem correct; loading Python packages...

Using cpu

Using 1 thread(s)

Preparing model and loading weights

Working on image 1 of 1: WMHsynthsegTset/T1_1.nii

Loading input volume and normalizing to [0,1]

Upscaling to target resolution

Pushing data through the CNN

Killed

Best,

Chuyue

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