Hi Rosemary, the seeds for those commands are set from recon-all. The
individual binaries do not seed themselves with a default value, so it’s
expected that mris_ca_label produces inconsistent results when run
independently (and without the -seed flag). The algorithm processes the surface
vertices in a random order to help prevent any spatial ordering effects, so the
given seed will initialize this order.
best,
Andrew
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosemary Nicholas
<rosemary.nicho...@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, July 23, 2018 at 1:22 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mris_ca_label seed
External Email - Use Caution
Hello,
I am running a dataset through version 6.0 of Freesurfer on Linux, extracting
results for both the Desikan atlas and our own atlas. When extracting the
stats for our atlas, the results were varying considerably (sometimes up to
10%) in test-retest runs.
The release notes for 4.5 indicate that the default setting for mris_ca_label
should use the same number as a seed, and therefore give the same results, but
it doesn't.
"The binaries in the recon-all stream which are subject to variability due to
usage of a random number generator (mris_smooth, mris_sphere,
mris_topology_fixer, mris_topo_fixer and mris_ca_label) are now seeded with the
same number, with the result being that repeated runs of the recon-all stream
on a subject on the same platform will always give identical results."
The issue seems to be resolved by adding -seed 1234 as a flag to mris_ca_label.
I would like to understand what this is actually doing though, before applying
it to all my data. What is the random number generator used for? What does
setting it to 1234 actually do? It isn't listed in the optional flagged
arguments. Is it just deciding which vertex is labeled first?
Here is how we are running it (in two independent scripts):
FIRST:
# autorecon1 including data conversion
recon-all -i $mprage/001 -autorecon1 -subjid $s
# autorecon2 with threshold adjustments
recon-all -seg-wlo 60 -seg-ghi 70 -autorecon2 -subjid $s
# autorecon3
recon-all -autorecon3 -subjid $s
THEN:
mris_ca_label $s $h sphere.reg
/g5/dcn/freesurfer_testing/subjects/"$h".rantaFL.gcs rantaFL.annot
modified to:
mris_ca_label -seed 1234 $s $h sphere.reg
/g5/dcn/freesurfer_testing/subjects/"$h".rantaFL.gcs rantaFL.annot
Thank you,
Rosemary Nicholas
Center for Neurodevelopmental and Imaging Research
Kennedy Krieger Institute
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