External Email - Use Caution 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. < [email protected]> 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 > > http://secure-web.cisco.com/1zsCYqW-9ZNH_a4OqKTDvB2UOigO8MgPwWbT3ku1d9jzOfNCgpcZaN1rPxN-XWDAd5subKsFyuEiWDKJdzewGTQ9r6wRDM-XDtsl9wqjyeYwEs61_-qGbANRz3Naq8i-xR5AsGNQDszCc5eFdd3AZ0KGKXgF9pNG1GLTrGMjFweXV5nVbq3_UVY8tISulnrwI5Bd2gJdGRTLIPN72qZyDr2x91JXRjmJeT3e7BYp6xOOu-pW4GLmZ4_gYlNp3gA-4wt1hNrxghI2jC9-3DAlJ4_hozlq-HSiZJaE5Z9SMZwfqnXd-uMoHV2_xpo0MU-oG3ZkmwM4UJXs924dzJin4bA/http%3A%2F%2Fwww.jeiglesias.com > > > > *From: *[email protected] < > [email protected]> on behalf of 赵楚越 < > [email protected]> > *Date: *Thursday, December 21, 2023 at 04:17 > *To: *[email protected] <[email protected]> > *Subject: *[Freesurfer] Killed procees during running WMH-SynthSeg > > * External Email - Use Caution * > > 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 > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1sb0ZclMvpCxRYF2NZFcPnIN1rkIXQtqjYw1-cEya0Tk_knQwgVBxu66AfeOWeMn5ht0ZEp_WeQjjxtnwoiF54sgXoGvrwqQr9-Jv9uEffugjG-rLlEr2vU2iTGlTHJDYF5-M8eGovohTAMUo_6UzuexnagViHLlzilETMzirEAesHVTNN2ZA0Lxq1VExBlM7i9bZ-3gowKNi67RhOAKsJvZ0ib0BPGo7kEN8RmwYywY3bhMyI8uO9TYDWQ-hZPaSFvDuVwcRqjcDBHK5bQSm-O8f2jzdOL-15hreuuWzGCy4YuARHGzldOZfn-1t7T9pgSgLFPULxiRnRq-acckSnQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1BgzuYEXfhU1cKMLtrye7uOUlCgi6l1amTUdS4-gqTDjoXzut_VwK0-uuB27PgsTsht32X4nYrdWvzprOqXeoj75Z_LitTg1ydsdmboo-JgAaZp0xGaX7L8tQr-1LSMv39GOMxqdPNwOe0VPeugcyOEjTB44HMPqK3EflhtUb5NGXRCI3eVGQ3RMgBjD-SlqiSNH7LROod9ex3itKkQf37i7AvNqlNrkEuyLe662AOLUo4aD4Ni489Uqe3PdCWli5oMluhmPJXI0Y_wXXCNLeGU9UPkPG3qRmEhuIgMEkdeJbTse816_02FZepnHLwetr_RUqig8x5LBocWBKDam0Kg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1BgzuYEXfhU1cKMLtrye7uOUlCgi6l1amTUdS4-gqTDjoXzut_VwK0-uuB27PgsTsht32X4nYrdWvzprOqXeoj75Z_LitTg1ydsdmboo-JgAaZp0xGaX7L8tQr-1LSMv39GOMxqdPNwOe0VPeugcyOEjTB44HMPqK3EflhtUb5NGXRCI3eVGQ3RMgBjD-SlqiSNH7LROod9ex3itKkQf37i7AvNqlNrkEuyLe662AOLUo4aD4Ni489Uqe3PdCWli5oMluhmPJXI0Y_wXXCNLeGU9UPkPG3qRmEhuIgMEkdeJbTse816_02FZepnHLwetr_RUqig8x5LBocWBKDam0Kg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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