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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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