Re: [Freesurfer] consistency in recon-all parallel pipeline

I tried with -threads instead, but it’s still inconsistent. See attached table with just ctx averages for 3 regions across 3 separate runs with bert.

Out of curiosity, what’s the difference between -threads and -parallel workflows?

Thanks, Mitch [A screenshot of a computer Description automatically generated]

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Date: Saturday, February 24, 2024 at 1:48 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline Can you try it with -threads instead? We don't typically use -parallel On 2/23/2024 2:44 PM, Horn, Mitchell Jacob wrote: This is all with ‘recon-all -parallel’

Thanks, Mitch

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Friday, February 23, 2024 2:30 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline

Do you run ‘recon-all -parallel’ or ‘recon-all –threads <nthreads>’?

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Horn, Mitchell Jacob Sent: Friday, February 23, 2024 12:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline

Bottom line is that when I run any FreeSurfer version 7+ in parallel on COS8 I get different results each time.

Thanks, Mitch

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Friday, February 23, 2024 11:03 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline

So, is the bottom line that when you run 7.4.1 on COS8 in parallel that you get (slightly) different results each time? On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote:

Hi FS Devs,

I’m experiencing unreproducible thickness results when running any 7+ version with parallelization enabled. Running recon-all without parallelization produces consistent thickness results. I’m running this in AlmaLinux8 (a library-equivalent downstream OS to CentOS8).

I’m attaching a table (table1) of 12 recons with bert:

1. 3 parallelized with CentOS8-compiled 7.4.1 2. 3 non-parallelized with CentOS8-compiled 7.4.1 3. 3 parallelized with CentOS7-compiled 7.4.1 4. 3 non-parallelized with CentOS7-compiled 7.4.1

I suspected the downstream CentOS8 libm was the culprit (because of testing I did this last 2023 summer). I ran 3 more recons parallelized with the CentOS7-compiled 7.4.1, but before running the recon-all command, set LD_PRELOAD to a copy of the CentOS7 libm libraries. The thickness results were then consistent, see the second table below (table2). I could not run this experiment on the CentOS8-compiled version, as that one is obviously not backward compatible with CentOS7 libm.

As a quick test of the OS-dependency, I submitted 3 parallel recons on MLSC with 7.3.3. Each reported different thickness. See table 3 (table3).

I’m asking if you can please confirm whether running any 7.+ version with parallelization is generating reproducible results for you in CentOS8 (or equivalent)?

P.S. - I tested 6.0 (CentOS6-compilation) with parallelization, and the results were consistent.

Best, Mitch

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