Re: [Freesurfer] Freesurfer 7.4.0 and CUDA versions (was Re: (no subject))

backwards compatible, I suggest you try installing Cuda 11 on your system > and see if it is recognized. > > - R. > > > On Sep 9, 2024, at 22:31, Matthew Lynch wrote: > > External Email - Use Caution > > > I run this command: > > mri_synthseg --i /mn

[Freesurfer] (no subject)

External Email - Use Caution I run this command: mri_synthseg --i /mnt/p/test/test-t2-3mm.nii --parc --robust --o /mnt/p/test and it fails with the following (partial) error message: Node: 'model_3/unet_conv_downarm_0_0/Conv3D' DNN library is not found. which I assume means it

Re: [Freesurfer] Killed procees during running WMH-SynthSeg

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 t

[Freesurfer] SynthSeg hippocampal quality control bias

External Email - Use Caution Dear Freesurfers, In using SynthSeg, I have observed that the quality control value for the hippocampus+amygdala seems to be directly correlated with the hippocampal volume. Higher QC values = higher volumes. There also seems to be an age effect on t

Re: [Freesurfer] recon-all-clinical out of memory error

to update that, > > $ cd $HOME > $ rm -f freesurfer > $ ln -s /usr/local/freesurfer/7.4.1 freesurfer > $ ls freesurfer > > ... check you have 7.4.1 ... > > $ cat freesurfer/build-stamp.txt > freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460 > > > - R. &

Re: [Freesurfer] recon-all-clinical out of memory error

en the > most efficient swap configuration won’t cause the machine to slow down to a > crawl depending upon what you are processing. It’s not a substitute for > having RAM to allocate to the VM. We have discussed increasing the > published memory system requirements for Freesurfer.

Re: [Freesurfer] recon-all-clinical out of memory error

mpute an average for the *total*memory* in use = (size of > physical RAM in use by synthseg + size of all swap files resident on disk > used by synthseg). > > - R. > > On Aug 10, 2023, at 16:08, Matthew Lynch wrote: > > External Email - Use Caution > > Here

Re: [Freesurfer] recon-all-clinical out of memory error

-gZjauJ7RkwcbkGLcSMi3C9yY2H1aGvyG3PPWD7Nmgl0oaVF8XgRWUAjud_IN5AuL3R33m2S9TDJoYQ/https%3A%2F%2Flearn.microsoft.com%2Fen-us%2Fwindows%2Fwsl%2Fwsl-config On Sat, Jul 29, 2023 at 6:27 AM Matthew Lynch wrote: > > I was able to get recon-all-clinical working with 16 Gb computer. > > I thought the problem might be Windows hogging memory, so I created a live

Re: [Freesurfer] recon-all-clinical out of memory error

-zVextcU0zdKZS40VUf8z_9D7dIRdwaA3dnuN6rKOop5o_IBd0Xhm4gQmczEdE5SepDZMz9a0BGgeAbf09f3ZzPyuMDZXLwyERiQRVQPyJMHuGClyrhtUC7d4NJuP_9KRBoqeR9BA4fwwkEHxZ3pS9vdU4gongLDl_1Q8VBZYKrm2q6TtMZRzrvRcidoPwmB4YdcPTSMGaOV0N2NodjXNNXXpmYqkMsO42oxmBpIBrh1lWHA/https%3A%2F%2Faskubuntu.com%2Fquestions%2F178712%2Fhow-to-increase-swap-space This worked. On Thu, Jul 13, 2023 at 3:28 PM Matthew Lynch wrote: > I do not have access to a computer with more RAM.

Re: [Freesurfer] recon-all-clinical out of memory error

, 2023 at 1:58 PM Fischl, Bruce R.,PHD < bfis...@mgh.harvard.edu> wrote: > External Email - Use Caution > > Can you try it on a computer with more ram? > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu>

[Freesurfer] recon-all-clinical out of memory error

External Email - Use Caution I am having trouble running the new recon-all-clinical module. I input 5mm T1 axial DICOM images and it fails in SynthSeg with what appears to be an out of memory error. I am running FreeSurfer 7.4.0 in WSL with Ubuntu 22 on a computer with 16 Gb RAM.