Hello, FreeSurfer Group,
What is the maximal matrix size for glm_fit process? How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes?
Thank you.
Xin
I don't think there is a maximum size. You would do the big analysis the same way as the small.
On 03/26/2017 07:54 PM, Wang, Xin wrote:
Hello, FreeSurfer Group,
What is the maximal matrix size for glm_fit process?
How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes?
Thank you.
Xin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you, Dr. Greve. when I ran >2000 subjects in Version 5.3, I received this error message "##ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 2000##" In your previous post about mri_glmfit, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033151..., I found #define FSGDF_NCLASSES_MAX 128 #define FSGDF_NVARS_MAX 128 #define FSGDF_NINPUTS_MAX 2000 Are these the maximum? The mri_glmfit is written in C. Could you send me a version of mri_glmfit code without limits? Thank you very much.
Xin
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 27, 2017 1:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] group analysis of large data sets
I don't think there is a maximum size. You would do the big analysis the same way as the small.
On 03/26/2017 07:54 PM, Wang, Xin wrote:
Hello, FreeSurfer Group,
What is the maximal matrix size for glm_fit process?
How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes?
Thank you.
Xin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
version 6 should be able to go up to 20,000
On 03/28/2017 11:45 AM, Wang, Xin wrote:
Thank you, Dr. Greve. when I ran >2000 subjects in Version 5.3, I received this error message "##ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 2000##" In your previous post about mri_glmfit, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033151..., I found #define FSGDF_NCLASSES_MAX 128 #define FSGDF_NVARS_MAX 128 #define FSGDF_NINPUTS_MAX 2000 Are these the maximum? The mri_glmfit is written in C. Could you send me a version of mri_glmfit code without limits? Thank you very much.
Xin
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 27, 2017 1:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] group analysis of large data sets
I don't think there is a maximum size. You would do the big analysis the same way as the small.
On 03/26/2017 07:54 PM, Wang, Xin wrote:
Hello, FreeSurfer Group,
What is the maximal matrix size for glm_fit process?
How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes?
Thank you.
Xin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Doug, three years later and an order of magnitude more subjects. Any chance you could raise the limit of maximum number of subjects further (>60K)?
Thanks a lot, Inge _________________________________________ Inge Kasbohm Amlien, PhD Center for Lifespan Changes in Brain and Cognition University of Oslo, Norway
On 28 Mar 2017, at 18:24, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
version 6 should be able to go up to 20,000
On 03/28/2017 11:45 AM, Wang, Xin wrote: Thank you, Dr. Greve. when I ran >2000 subjects in Version 5.3, I received this error message "##ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 2000##" In your previous post about mri_glmfit, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033151..., I found #define FSGDF_NCLASSES_MAX 128 #define FSGDF_NVARS_MAX 128 #define FSGDF_NINPUTS_MAX 2000 Are these the maximum? The mri_glmfit is written in C. Could you send me a version of mri_glmfit code without limits? Thank you very much.
Xin
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 27, 2017 1:47 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] group analysis of large data sets
I don't think there is a maximum size. You would do the big analysis the same way as the small.
On 03/26/2017 07:54 PM, Wang, Xin wrote: Hello, FreeSurfer Group,
What is the maximal matrix size for glm_fit process?
How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes?
Thank you.
Xin
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ 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.
I put one here that can go up to 80k https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit.80k
On 4/21/2020 3:15 PM, Inge Amlien wrote:
External Email - Use Caution
Hi Doug, three years later and an order of magnitude more subjects. Any chance you could raise the limit of maximum number of subjects further (>60K)?
Thanks a lot, Inge _________________________________________ Inge Kasbohm Amlien, PhD Center for Lifespan Changes in Brain and Cognition University of Oslo, Norway
On 28 Mar 2017, at 18:24, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
version 6 should be able to go up to 20,000
On 03/28/2017 11:45 AM, Wang, Xin wrote:
Thank you, Dr. Greve. when I ran >2000 subjects in Version 5.3, I received this error message "##ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 2000##" In your previous post about mri_glmfit, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033151..., I found #define FSGDF_NCLASSES_MAX 128 #define FSGDF_NVARS_MAX 128 #define FSGDF_NINPUTS_MAX 2000 Are these the maximum? The mri_glmfit is written in C. Could you send me a version of mri_glmfit code without limits? Thank you very much.
Xin
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 27, 2017 1:47 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] group analysis of large data sets
I don't think there is a maximum size. You would do the big analysis the same way as the small.
On 03/26/2017 07:54 PM, Wang, Xin wrote:
Hello, FreeSurfer Group,
What is the maximal matrix size for glm_fit process?
How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes?
Thank you.
Xin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Douglas N. Greve -
Inge Amlien -
Wang, Xin