Dear all,
I am trying to run a group analysis between 2 groups of subjects. I did the mris_preproc and mri_surf2surf steps. When I set up my mri_glmfit, the end of the output is:
Reshaping mriglm->mask... search space = 74485.691578 DOF = 1344 Starting fit and test Fit completed in 0.481417 minutes Computing spatial AR1 on surface Residual: ar1mn=0.996928, ar1std=0.000586, gstd=7.275170, fwhm=17.131715 Writing results wholegrp_contrast maxvox sig=1e+10 F=33202.6 at index 0 0 0 seed=1396057719 mri_glmfit done
Now, from past experience, I know that the search space I get here is large. Why does my maxvox sig say infinite? Am I missing something? Has this happened to others?
Thanks Koushik
what does the max vox have to do with the search space? I'm not sure what the problem is here. dough
On 04/01/2014 05:05 PM, Govindarajan, Koushik Athreya wrote:
Dear all,
I am trying to run a group analysis between 2 groups of subjects. I did the mris_preproc and mri_surf2surf steps. When I set up my mri_glmfit, the end of the output is:
Reshaping mriglm->mask…
search space = 74485.691578
DOF = 1344
Starting fit and test
Fit completed in 0.481417 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.996928, ar1std=0.000586, gstd=7.275170, fwhm=17.131715
Writing results
wholegrp_contrast
maxvox sig=1e+10 F=33202.6 at index 0 0 0 seed=1396057719
mri_glmfit done
Now, from past experience, I know that the search space I get here is large. Why does my maxvox sig say infinite? Am I missing something? Has this happened to others?
Thanks
Koushik
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I proceeded to do a Monte Carlo simulation with this glm and pretty much the entire brain lit up. That is why I was wondering if the max vox being so large or the search space has anything to do with it. I used a vertex-wise p-value of 0.001 and a cluster-wise p-value of 0.05.
Thanks Koushik
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, April 01, 2014 4:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit question
what does the max vox have to do with the search space? I'm not sure what the problem is here. dough
On 04/01/2014 05:05 PM, Govindarajan, Koushik Athreya wrote:
Dear all,
I am trying to run a group analysis between 2 groups of subjects. I did the mris_preproc and mri_surf2surf steps. When I set up my mri_glmfit, the end of the output is:
Reshaping mriglm->mask...
search space = 74485.691578
DOF = 1344
Starting fit and test
Fit completed in 0.481417 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.996928, ar1std=0.000586, gstd=7.275170, fwhm=17.131715
Writing results
wholegrp_contrast
maxvox sig=1e+10 F=33202.6 at index 0 0 0 seed=1396057719
mri_glmfit done
Now, from past experience, I know that the search space I get here is large. Why does my maxvox sig say infinite? Am I missing something? Has this happened to others?
Thanks
Koushik
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvar d.edu/mailman/listinfo/freesurfer&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A& r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=kGMeR2ywj8DA uHR01yI9QTMsjMPS46IV6f7syTjaz%2Bg%3D%0A&s=81b9e1c427d7eb86e493a947c849 88d7d2cfd16a9f560b17fef367fab26a81d9
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://urldefense.proofpoint.com/v1/url?u=https://gate.nmr.mgh.harvard.edu/... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v1/url?u=ftp://surfer.nmr.mgh.harvard.edu/...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu/...
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 https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianc... . 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.
No it should not. You should check your data and design to make sure that it makes sense doug
On 04/01/2014 05:46 PM, Govindarajan, Koushik Athreya wrote:
I proceeded to do a Monte Carlo simulation with this glm and pretty much the entire brain lit up. That is why I was wondering if the max vox being so large or the search space has anything to do with it. I used a vertex-wise p-value of 0.001 and a cluster-wise p-value of 0.05.
Thanks Koushik
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, April 01, 2014 4:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit question
what does the max vox have to do with the search space? I'm not sure what the problem is here. dough
On 04/01/2014 05:05 PM, Govindarajan, Koushik Athreya wrote:
Dear all,
I am trying to run a group analysis between 2 groups of subjects. I did the mris_preproc and mri_surf2surf steps. When I set up my mri_glmfit, the end of the output is:
Reshaping mriglm->mask...
search space = 74485.691578
DOF = 1344
Starting fit and test
Fit completed in 0.481417 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.996928, ar1std=0.000586, gstd=7.275170, fwhm=17.131715
Writing results
wholegrp_contrast
maxvox sig=1e+10 F=33202.6 at index 0 0 0 seed=1396057719
mri_glmfit done
Now, from past experience, I know that the search space I get here is large. Why does my maxvox sig say infinite? Am I missing something? Has this happened to others?
Thanks
Koushik
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvar d.edu/mailman/listinfo/freesurfer&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A& r=4ebx%2BU4XzNnu4XA8t53Lt0n%2FTCuxbfN4Z1deUmAFsLg%3D%0A&m=kGMeR2ywj8DA uHR01yI9QTMsjMPS46IV6f7syTjaz%2Bg%3D%0A&s=81b9e1c427d7eb86e493a947c849 88d7d2cfd16a9f560b17fef367fab26a81d9
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://urldefense.proofpoint.com/v1/url?u=https://gate.nmr.mgh.harvard.edu/... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v1/url?u=ftp://surfer.nmr.mgh.harvard.edu/...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu/...
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 https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianc... . 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
-
Douglas N Greve -
Govindarajan, Koushik Athreya