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<mailto: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<mailto: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<mailto: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<mailto:julie.jj.ot...@gmail.com>> wrote:
<recon-all.log>
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