Hi Xin,

In Freesurfer 7.3, recon-all is running with ‘-norandomness’ by default unless ‘-randomness’ is specified in the command line.

‘-randomness’ uses current time and date as the seed for random number generation. This results in slightly different surfaces each run.

‘-norandomness’ ensures consistency in surface creation. By default, all seed critical binaries will run with identical seeds ‘1234’, which can be changed with ‘-rng-seed <seed>’.  Here is the list of binaries that recon-all passes the seed:

mri_normalize

mris_smooth

mris_sphere

mris_fix_topology

mris_topo_fixer

mris_curvature

mris_ca_label

mri_segstats

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Xin Qi
Sent: Tuesday, November 15, 2022 8:50 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] about using -norandomness flag with recon-all

        External Email - Use Caution        

Hello Freesurfer Team:

Because of ensuring that results are exactly the same from run to run, norandomness flag is used with recon-all. 

To better understand the randomness, we have a few questions listed below. 

1. Which algorithms inside the recon-all use the seeded random number? 

And what randomness is about?

2. Is there a way to use a seed value to ensure the same data can be reproduced?

3. Whether we are compromising anything by going with the non-random option?

Thank you very much for your time and looking forward to hearing from you.

Best regards

Xin