You can also try editing the wm.mgz or filled.mgz to remove the defect.
See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 10/3/2023 5:23 AM, Pål Gunnar Larsson wrote:
External Email - Use Caution
OK.
Did make a new setup with 16Gb. Restarted. Hope I can give you
positive feedback tomorrow.
Best
Pål
Pål G. Larsson M.D., PhD.
Senior Medical Officer
Department of Neurosurgery
Division of Surgery and Clinical Neuroscience
Oslo University Hospital
Po.box 4950 Nydalen
0424 Oslo
Norway
Tel: (+47) 23074407
Mobile: (+47) 93429791
E-mail: p...@ous-hf.no
Ikke sensitiv
*Fra:*fsbuild <fsbu...@contbay.com>
*Sendt:* 3. oktober 2023 08:29
*Til:* freesurfer@nmr.mgh.harvard.edu
*Kopi:* Pål Gunnar Larsson <p...@ous-hf.no>
*Emne:* Re: [Freesurfer] Slow processing of large defect
If your host machine has 32G of RAM, then it should work to give the
VM 16G or perhaps even 24G of RAM.
If most all swap space is in use, then it’s likely something is
under-running or exhausting the available physical RAM. Some
machines start to swap what’s in memory out to disk files when only
80% of RAM is in use. But disk I/O from loading swap files in/out of
memory can cause the machine to slow down or thrash and never finish
processing. With no consequential or RAM hungry applications running
on the host, then the host should be able to essentially run idle with
8G of RAM leaving 24G to assign to the VM.
- R.
On Oct 3, 2023, at 02:01, Pål Gunnar Larsson <p...@ous-hf.no> wrote:
* External Email - Use Caution *
Thank you for fast reply.
The computer has 32Gb. The virtual machine has 8Gb. According to
‘top’ all is used, except 140Mb. Swap has 1Gb of which 780Mb is
used. Does swapping use lots of CPU? It is 100% most of the time.
*Fra:*fsbuild <fsbu...@contbay.com <mailto:fsbu...@contbay.com>>
*Sendt:*3. oktober 2023 04:33
*Til:*freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Kopi:*Pål Gunnar Larsson <p...@ous-hf.no <mailto:p...@ous-hf.no>>
*Emne:*Re: [Freesurfer] Slow processing of large defect
Not clear if "8G of RAM" below means 8G is assigned to the VM, or
the host machine has 8G RAM total. Assuming the VM has ~8G
assigned then the host should have 16-24G RAM total.
It reads like the VM is thrashing, e.g., swapping out to disk due
to lack of RAM - which can cause a crash. I would try running
the VM on a host machine that can provide more RAM. So if the VM
is currently running with 8G, then try doubling it to 16G (on a
host with at least 24 or 32G RAM)..
- R.
On 10/2/23 10:31, Pål Gunnar Larsson (p...@ous-hf.no
<mailto:p...@ous-hf.no>) wrote:
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Hello
I am running FS 7.4.1 on Ubuntu 22.10 on Virtualbox 21.10,
having 8Gb of ram.
I am running a child-MRI where I got a message about a large
defect which would run slowly or crash. FS is still running
after more than 10 days (70%-100% CPU use), but there are
nothing written to disk for 10 days. It is working on
retesselation of defect 162.
Is there any reason to wait it out? Or will the results be
unpredictable?
Best
Pål G. Larsson
Ikke sensitiv
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