External Email - Use Caution Hi Andrew,
Thanks! So as long as we set the seed in mris_ca_label the results should be consistent, right? Would there be any difference to running it this way (independently) and running it with recon-all? Thanks, Rosemary On Mon, Jul 23, 2018 at 6:27 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > 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 > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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