External Email - Use Caution Hi,
I just wanted to check in with my questions below? Thanks! Julie On Thu, 10 Nov 2022 at 17:03, Julie Ottoy <julie.jj.ot...@gmail.com> wrote: > 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/1rujhgNgElL31tpcA9BnZ3L56mYLwCh4xAlmyhmm9zlCxfAeh4HOJcTsWyw5c54NNsQCMfJ2wDB479cOYkURjTKsK8XXQdMtlJb2n_lBKeXPXA-VoSvo3zqGZJcHIu3d4ztuj_btoGmfPYWO7vW38rue9H1qGJv2kRAlRpJ4J2H0c_mZ31AEm9s2EBfTCuSOw-ObZg_xJVtsYMPp8AIOAkxrRcAu_GClXSYIkuY4sPRACR9-IbPfu4Jo2MWVzfcQch8BKUYxscU8uFwKKHpeQk8URGq7PZTJcp5bqMiqVpa93bGr-G3Y5vXVqeP7bF6XGFwlyrM6w78_2JW_30jxQCg/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/1b3AP1bzETo1Db5FeVbB6yv6eIETXP28nFnyNbN1GijLzf7RhriwyExBPaE0E_7wP7f3mfiRYNbzojWkKPaHAYZR5NSsQJF9EgQnF17iERtjb8c9I_NLCCDvtnwhcdOxx1w6y8j0jJ1opf7OqL_EU-rLyCW1HYbC2mjGfhHaCveY7iNGqtM2-SMXfonqbvhScnju1mOnGrZtx7GRhXi7k4DFqoW1yN1q8L3M5uiU5zOZpCnikhf4IhM4gopy8OqIno0mCNNArYMKPHPkHw43R6nd5wLQnvRqWCfZyO-D65Ty3IFtsHi8YbM81nVJqBHr_IHc3gykYCeQk8u5Tcj3ekw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> < >> https://secure-web.cisco.com/1b3AP1bzETo1Db5FeVbB6yv6eIETXP28nFnyNbN1GijLzf7RhriwyExBPaE0E_7wP7f3mfiRYNbzojWkKPaHAYZR5NSsQJF9EgQnF17iERtjb8c9I_NLCCDvtnwhcdOxx1w6y8j0jJ1opf7OqL_EU-rLyCW1HYbC2mjGfhHaCveY7iNGqtM2-SMXfonqbvhScnju1mOnGrZtx7GRhXi7k4DFqoW1yN1q8L3M5uiU5zOZpCnikhf4IhM4gopy8OqIno0mCNNArYMKPHPkHw43R6nd5wLQnvRqWCfZyO-D65Ty3IFtsHi8YbM81nVJqBHr_IHc3gykYCeQk8u5Tcj3ekw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >> . >> >
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