Re: [Freesurfer] mris_ca_label seed
External Email - Use Caution Great, thank you! On Tue, Jul 24, 2018 at 12:28 PM, Bruce Fischl 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 >> 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: on behalf of >> Rosemary Nicholas >> Reply-To: FS Help >> Date: Monday, July 23, 2018 at 1:22 PM >> To: FS Help >> 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 doe
Re: [Freesurfer] mris_ca_label seed
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 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: on behalf of Rosemary Nicholas Reply-To: FS Help Date: Monday, July 23, 2018 at 1:22 PM To: FS Help 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. ___ 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.
Re: [Freesurfer] mris_ca_label seed
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 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: * on behalf of Rosemary > Nicholas > *Reply-To: *FS Help > *Date: *Monday, July 23, 2018 at 1:22 PM > *To: *FS Help > *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. > > ___ 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.
Re: [Freesurfer] mris_ca_label seed
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: on behalf of Rosemary Nicholas Reply-To: FS Help Date: Monday, July 23, 2018 at 1:22 PM To: FS Help 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.
[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.
[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.
