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 AHOOPES@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-bounces@nmr.mgh.harvard.edu on behalf of Rosemary Nicholas rosemary.nicholas@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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External Email - Use Caution

Great, thank you!

On Tue, Jul 24, 2018 at 12:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

no, they should be the same

On Tue, 24 Jul 2018, Rosemary Nicholas wrote:

...

    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 AHOOPES@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-bounces@nmr.mgh.harvard.edu> on behalf of
  Rosemary Nicholas <rosemary.nicholas@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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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.

---

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.