External Email - Use Caution Hi,
Yes you are right! Taking out the -parallel solved the issue! Does this mean v7 longitudinal recon-all does not support this flag? I have one other question, any help would be appreciated. I ran the baseline recon-all with the -bv (big ventricles) flag. Should I add this flag for longitudinal processing as well, or will it not matter? Thanks again for your support, Best wishes Julie On Wed, 9 Nov 2022 at 15:36, Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: > Hi Julie, > > > > I noticed that you were running recon-all with ‘-parallel’ flag. It is > causing the error. > > > > The process should work if you remove ‘-parallel’ from recon-all command. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Julie Ottoy > *Sent:* Tuesday, November 8, 2022 9:27 AM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; fsbuild < > fsbu...@contbay.com> > *Subject:* [Freesurfer] Fwd: Longitudinal FS pipeline consistently > interrupts at -Sphere for all participants > > > > * External Email - Use Caution * > > Hi FS team, > > > > Just wanted to follow up with my question below. Thanks! > > Julie > > ---------- Forwarded message --------- > From: *Julie Ottoy* <julie.jj.ot...@gmail.com> > Date: Fri, 4 Nov 2022 at 00:11 > Subject: Re: [Freesurfer] Longitudinal FS pipeline consistently interrupts > at -Sphere for all participants > To: fsbuild <fsbu...@contbay.com> > > > > Hi Fsbuild team, > > > > Thank you for your reply. Sorry for the confusion, my system was actually > Linux, not Windows. It did *not* run on top of Windows (sorry again for > the confusion). > > In any case, I tried both the longitudinal pipeline FS v7.1.1 and v7.2 > consistently on Linux. I also used two different machines (our institute > server as well as ComputeCanada, hence I do not believe it's a memory > issue). Each run got stuck at the -Sphere x.long.x step as indicated in my > previous email. Interestingly, I tried today with the longitudinal FS > v6.0.0 (kept all the rest the same) and it ran fine! Could there be any bug > in the v7 series for longitudinal processing that was not present in the v6 > series? I tried on two different types of input T1w data acquired from > different centers and they point to the same issue => -Sphere error in > x.long.x for v7 , while it runs fine for v6. Please see attached log files > and screenshots for both. > > > > I am also thinking if it would be ok to run the longitudinal with v6 since > we ran the baseline data with v7.2. Could you please advise on this? > > > > Last, I was wondering if there is a way to receive more detailed log/error > files? As indicated from my previous email and screenshots, the code just > exited at Sphere but did not indicate why it went wrong there. > > > > Thank you for your help! > > Best regards > > Julie > > > > On Wed, 2 Nov 2022 at 17:02, fsbuild <fsbu...@contbay.com> wrote: > > One way we’ve seen recon-all eventually fail running on Linux hosted on > Windows is whatever is virtualizing Linux to run on top of the Windows OS - > simply runs out of memory at some point in the processing pipeline. That > can result in a message in the recon-all.log like a file was not found, > i.e., a computation fails and the results are not saved in a file that > later on is expected to be found, opened and read. I don’t see messages > like that in your log. > > > > It might be helpful to know more about how you are running Linux on > windows, e.g., if you are using the built-in Windows Subsystem for Linux > (WSL) or using a VM running on something like VirtualBox. > > > > You could also send along the output in the linux terminal from: > > $ cat /etc/os-release > > $ cat $FREESURFER_HOME/build-stamp.txt > > > > - R. > > > > On Nov 2, 2022, at 15:03, Julie Ottoy <julie.jj.ot...@gmail.com> wrote: > > > > <recon-all.log> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/135XF05YrgXN9hdbbM4w7HVq0tQXXsoAh1ELrzudg_qqq4RH4p8yJnSLbNCbSbEcz93BkEoPEFd6jZIaujpNPD-hH0uyaDp18RKPIcwL_Vr1bBraTZbqIp2sHFOz-kHdG_pUVOkJZ6QWtXqnEjlrDP5pEz7w_0H5cfJ9NmCzPcZQckz168TeDH-oU4G0URqWm3veHmY2MC0jvREO7Hfigvk5FnYQNHbuJGl3nCVoQ2iLb5pg32-KwN7sY7rwB-vVEL9JOMM1OQxF1Ere5x_iah1wXaA1ZUxTqvasx5Ygbw-b5C7oLtrVW8tltE6-9pD08/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/13Qt8VtY_dV-915csZ35HNAIuYNN9RpOwJZtOjf_4L-NbViAhC85LZtxuDkvaioMQrVt5gNixahNwIho4i-o75TLIWJcoYEgarvH6pOjnfVoCLrmcUJuopxk-q2cKv3J4qRTrWWfubtxv6hq3Ko_M8LBQkeBg-_4L-Nxt_cAxi5PiMWPXfG3ajHBEbXTkQqJs19u9phfpuTwaU5hncMDK4bM1DZE66Ijw5zDkWWTCJgcVeWIKVQeFxyTP6k-HGMNHeXBpWLHUtQ3NFdxnLQUS1afyu7MPiuku9JmH2jiqHORUOKWKHiLxEHcmTk4D4rUk/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/13Qt8VtY_dV-915csZ35HNAIuYNN9RpOwJZtOjf_4L-NbViAhC85LZtxuDkvaioMQrVt5gNixahNwIho4i-o75TLIWJcoYEgarvH6pOjnfVoCLrmcUJuopxk-q2cKv3J4qRTrWWfubtxv6hq3Ko_M8LBQkeBg-_4L-Nxt_cAxi5PiMWPXfG3ajHBEbXTkQqJs19u9phfpuTwaU5hncMDK4bM1DZE66Ijw5zDkWWTCJgcVeWIKVQeFxyTP6k-HGMNHeXBpWLHUtQ3NFdxnLQUS1afyu7MPiuku9JmH2jiqHORUOKWKHiLxEHcmTk4D4rUk/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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