Hi Julie,

Sorry for the late response. You will need to pass -bv (big ventricles) flag to cross, base, and long processes.

Best,

Yujing

From: Julie Ottoy <julie.jj.ottoy@gmail.com>
Sent: Tuesday, November 15, 2022 11:56 AM
To: Huang, Yujing <YHUANG43@mgh.harvard.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants

        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.ottoy@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 <YHUANG43@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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 <fsbuild@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.ottoy@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 <fsbuild@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 <fsbuild@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.ottoy@gmail.com> wrote:

<recon-all.log>

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .