Hello,
Our group is interested in running the hippocampal segmentation on the PING dataset. That dataset was already Freesurfed, v4.5. When we try to just run the –hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) it dies looking for a number of files that were not a part of v.4.5.
One option is to start from scratch with v6: recon-all -all -s bert -hippocampal-subfields-T1
However, this seems to be a bad option because the quality control on the ~1500 brains is already completed for the original FS run.
My question is, are there certain flags from –autorecon2 and –autorecon3 that we could run so we don’t have to re-freesurf everything, or would it be better to just run –all? In other words, what are the minimum files needed to get hippocampal-subfields-T1 to run?
Thanks for any suggestions!
Anthony
— Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick@fiu.edu Webpage: http://myweb.fiu.edu/adick Join the Society for the Study of Human Development: http://www.sshdonline.org
Dear Anthony, Can you please send us a sample subject directory (the mri dir is enough, i don't need the surfaces), so i can play with it and see if there's anything we can do? Cheers E
Sent from my phone, please excuse brevity and typos
From: Anthony Dick Sent: Thursday, June 1, 16:40 Subject: [Freesurfer] running hippocampal segmentation on PING To: Freesurfer support list
Hello,
Our group is interested in running the hippocampal segmentation on the PING dataset. That dataset was already Freesurfed, v4.5. When we try to just run the –hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) it dies looking for a number of files that were not a part of v.4.5.
One option is to start from scratch with v6: recon-all -all -s bert -hippocampal-subfields-T1
However, this seems to be a bad option because the quality control on the ~1500 brains is already completed for the original FS run.
My question is, are there certain flags from –autorecon2 and –autorecon3 that we could run so we don’t have to re-freesurf everything, or would it be better to just run –all? In other words, what are the minimum files needed to get hippocampal-subfields-T1 to run?
Thanks for any suggestions!
Anthony
—
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: adick@fiu.edu
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development: http://www.sshdonline.org
Hello Eugenio,
Thanks for responding. The PING dataset is a public use dataset but requires direct request from PING. If I share it that would violate the data use agreement: https://pingstudy.ucsd.edu/legal.html. You can get the data but would need to go through the proper channels with PING, and that takes time.
However, I could tell you what files are in the MRI directory? Or provide other information that might be helpful? If you know what files the segmentation needs I could possibly just run those specific flags.
Anthony
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, June 2, 2017 at 7:10 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] running hippocampal segmentation on PING
Dear Anthony, Can you please send us a sample subject directory (the mri dir is enough, i don't need the surfaces), so i can play with it and see if there's anything we can do? Cheers E
Sent from my phone, please excuse brevity and typos
From: Anthony Dick Sent: Thursday, June 1, 16:40 Subject: [Freesurfer] running hippocampal segmentation on PING To: Freesurfer support list
Hello,
Our group is interested in running the hippocampal segmentation on the PING dataset. That dataset was already Freesurfed, v4.5. When we try to just run the –hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) it dies looking for a number of files that were not a part of v.4.5.
One option is to start from scratch with v6: recon-all -all -s bert -hippocampal-subfields-T1
However, this seems to be a bad option because the quality control on the ~1500 brains is already completed for the original FS run.
My question is, are there certain flags from –autorecon2 and –autorecon3 that we could run so we don’t have to re-freesurf everything, or would it be better to just run –all? In other words, what are the minimum files needed to get hippocampal-subfields-T1 to run?
Thanks for any suggestions!
Anthony
—
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: adick@fiu.edu
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development: http://www.sshdonline.org
Yes, please, send me a list of files. And, if you don’t mind, please send me aseg.mgz and wmparc.mgz, if they exist - they are segmentations, so you won’t be violating the agreement ;-) Another option is sending me bert. Cheers, /E
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 2 Jun 2017, at 14:16, Anthony Dick <adick@fiu.edumailto:adick@fiu.edu> wrote:
Hello Eugenio,
Thanks for responding. The PING dataset is a public use dataset but requires direct request from PING. If I share it that would violate the data use agreement: https://pingstudy.ucsd.edu/legal.html. You can get the data but would need to go through the proper channels with PING, and that takes time.
However, I could tell you what files are in the MRI directory? Or provide other information that might be helpful? If you know what files the segmentation needs I could possibly just run those specific flags.
Anthony
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, June 2, 2017 at 7:10 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] running hippocampal segmentation on PING
Dear Anthony, Can you please send us a sample subject directory (the mri dir is enough, i don't need the surfaces), so i can play with it and see if there's anything we can do? Cheers E
Sent from my phone, please excuse brevity and typos
From: Anthony Dick Sent: Thursday, June 1, 16:40 Subject: [Freesurfer] running hippocampal segmentation on PING To: Freesurfer support list
Hello,
Our group is interested in running the hippocampal segmentation on the PING dataset. That dataset was already Freesurfed, v4.5. When we try to just run the –hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) it dies looking for a number of files that were not a part of v.4.5.
One option is to start from scratch with v6: recon-all -all -s bert -hippocampal-subfields-T1
However, this seems to be a bad option because the quality control on the ~1500 brains is already completed for the original FS run.
My question is, are there certain flags from –autorecon2 and –autorecon3 that we could run so we don’t have to re-freesurf everything, or would it be better to just run –all? In other words, what are the minimum files needed to get hippocampal-subfields-T1 to run?
Thanks for any suggestions!
Anthony
—
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: adick@fiu.edumailto:adick@fiu.edu
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development: http://www.sshdonline.org
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Hi Anthony do you have any data that you have run through that version of FS? Or maybe you can run another dataset through it? It doesn't matter to us what subject it is
cheers Bruce
On Fri, 2 Jun 2017, Anthony Dick wrote:
Hello Eugenio,
Thanks for responding. The PING dataset is a public use dataset but requires direct request from PING. If I share it that would violate the data use agreement: https://pingstudy.ucsd.edu/legal.html. You can get the data but would need to go through the proper channels with PING, and that takes time.
However, I could tell you what files are in the MRI directory? Or provide other information that might be helpful? If you know what files the segmentation needs I could possibly just run those specific flags.
Anthony
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, June 2, 2017 at 7:10 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] running hippocampal segmentation on PING
Dear Anthony, Can you please send us a sample subject directory (the mri dir is enough, i don't need the surfaces), so i can play with it and see if there's anything we can do? Cheers E
Sent from my phone, please excuse brevity and typos
From: Anthony Dick Sent: Thursday, June 1, 16:40 Subject: [Freesurfer] running hippocampal segmentation on PING To: Freesurfer support list
Hello,
Our group is interested in running the hippocampal segmentation on the PING dataset. That dataset was already Freesurfed, v4.5. When we try to just run the –hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) it dies looking for a number of files that were not a part of v.4.5.
One option is to start from scratch with v6: recon-all -all -s bert -hippocampal-subfields-T1
However, this seems to be a bad option because the quality control on the ~1500 brains is already completed for the original FS run.
My question is, are there certain flags from –autorecon2 and –autorecon3 that we could run so we don’t have to re-freesurf everything, or would it be better to just run –all? In other words, what are the minimum files needed to get hippocampal-subfields-T1 to run?
Thanks for any suggestions!
Anthony
—
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: adick@fiu.edu
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development: http://www.sshdonline.org
freesurfer@nmr.mgh.harvard.edu
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Anthony Dick -
Bruce Fischl -
Iglesias Gonzalez, Eugenio