Thank you, I have three follow up questions:
Threshold is -log10(p), why are negative values showing up on the display?
I am using fsaverage to display my results, would it make any difference if I created my own average subject based on the analysis?
Is it possible to export the voxel-by-voxel intensities (or the brain surface data) used in Freesurfer's analysis; and then re-import the some external analysis results back to Freesurfer format for display purposes?
Cole
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: Monday, January 22, 2007 11:56 AM To: Reschke, Cole Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] interpret analysis results
The values are -log10(p), so p < .01 would require a threshold of 2, etc. I don't use t, z, or F because I have not memorized the various tables that convert them to p:). The sig will map to any surface, including pial.
doug
Reschke, Cole wrote:
First, thanks to Doug for all his help up to this point.
Next, I have three questions. In my analysis, I used the -paired-diff and -osgm options in mris_preproc and mri_glmfit, respectively. I have successfully loaded sig.mgh onto the inflated surface.
Are the values from the color chart [-5,5] representative of a t-score or an F-score (t^2)?
I adjust the threshold by changing the 'Min' value in the 'Configure Overlay Display'?
Ex. If Min ==3, then p < 0.001 ?
Is the sig.mgh created solely for the inflated surface, or is it able to be uploaded on others (pial, wm, etc.)?
Thank you,
Cole
Cole Reschke
Data Manager, PET Center
Banner Alzheimer Institute
Banner Good Samaritan Medical Center
Phone: (602) 239-4868
________________________________
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Reschke, Cole wrote:
Thank you, I have three follow up questions:
Threshold is -log10(p), why are negative values showing up on the display?
Sorry, the formula is not quite right, it is -sign(t)*log10(p), where t is the t ratio for the t-test. It's sign is the sign of the contrast.
I am using fsaverage to display my results, would it make any difference if I created my own average subject based on the analysis?
It won't really have an effect on the analysis.
Is it possible to export the voxel-by-voxel intensities (or the brain surface data) used in Freesurfer's analysis; and then re-import the some external analysis results back to Freesurfer format for display purposes?
Yes. The input to mri_glmfit (ie, arg of --y) is just such a file. If you make your analysis have the same size and don't swap the voxels around, then you can can reimport.
dopug
Cole
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: Monday, January 22, 2007 11:56 AM To: Reschke, Cole Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] interpret analysis results
The values are -log10(p), so p < .01 would require a threshold of 2, etc. I don't use t, z, or F because I have not memorized the various tables that convert them to p:). The sig will map to any surface, including pial.
doug
Reschke, Cole wrote:
First, thanks to Doug for all his help up to this point.
Next, I have three questions. In my analysis, I used the -paired-diff and -osgm options in mris_preproc and mri_glmfit, respectively. I have successfully loaded sig.mgh onto the inflated surface.
Are the values from the color chart [-5,5] representative of a t-score or an F-score (t^2)?
I adjust the threshold by changing the 'Min' value in the 'Configure Overlay Display'?
Ex. If Min ==3, then p < 0.001 ?
Is the sig.mgh created solely for the inflated surface, or is it able to be uploaded on others (pial, wm, etc.)?
Thank you,
Cole
Cole Reschke
Data Manager, PET Center
Banner Alzheimer Institute
Banner Good Samaritan Medical Center
Phone: (602) 239-4868
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
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Reschke, Cole