Hello,
I have a two groups comparison design, and I was wondering if there is any easy way to compute an average thickness file per group (in order to be able to overlay mean thickness values on my average subject). Is there an existing command or matlab function to do it? If yes, would I also be able to do a standard deviation file using the same command?
Many thanks,
Marie Schaer
If you are going to run mri_glmfit on the thicknesses in order to do stats, then this should/could be one of the outputs. If you make two groups in the fsgd file, then the first frame of the beta.mgh file will be the average thickness for group1, and the 2nd frame will be group 2.
use something like:
mri_convert beta.mgh group1.mgh --frame 0 mri_convert beta.mgh group2.mgh --frame 1 doug
Marie Schaer wrote:
Hello,
I have a two groups comparison design, and I was wondering if there is any easy way to compute an average thickness file per group (in order to be able to overlay mean thickness values on my average subject). Is there an existing command or matlab function to do it? If yes, would I also be able to do a standard deviation file using the same command?
Many thanks,
Marie Schaer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug Greve,
Many thanks for your reply, however when I overlay group1.mgh and group2.mgh on my average subject, they look pretty similar.
So I read it in matlab, using load_mgh(group*.mgh), which gave me files having exactly the same structure as beta.mgh (size of 23406 x 1 x 7 x 6). The content of the 3 files (beta.mgh, group1.mgh and group2.mgh) is also exactly identical.
So if I understood well, information is coded as 7 times 23406 vertices (which in total makes the 163842 vertices corresponding to my average surface), and for each vertex I have 6 values.
I have thus two questions on beta.mgh: 1) The first two values look like thickness measurements, and thus may be the average thickness for group 1 and group 2, is it right?
2) Can I also ask you what are the 4 other values?
Thank you very much for your help,
Marie Schaer
On Feb 9, 2007, at 7:22 PM, Doug Greve wrote:
If you are going to run mri_glmfit on the thicknesses in order to do stats, then this should/could be one of the outputs. If you make two groups in the fsgd file, then the first frame of the beta.mgh file will be the average thickness for group1, and the 2nd frame will be group 2.
use something like:
mri_convert beta.mgh group1.mgh --frame 0 mri_convert beta.mgh group2.mgh --frame 1 doug
Marie Schaer wrote:
Hello,
I have a two groups comparison design, and I was wondering if there is any easy way to compute an average thickness file per group (in order to be able to overlay mean thickness values on my average subject). Is there an existing command or matlab function to do it? If yes, would I also be able to do a standard deviation file using the same command?
Many thanks,
Marie Schaer _______________________________________________ Freesurfer mailing list 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 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
Marie Schaer wrote:
Dear Doug Greve,
Many thanks for your reply, however when I overlay group1.mgh and group2.mgh on my average subject, they look pretty similar.
So I read it in matlab, using load_mgh(group*.mgh), which gave me files having exactly the same structure as beta.mgh (size of 23406 x 1 x 7 x 6). The content of the 3 files (beta.mgh, group1.mgh and group2.mgh) is also exactly identical.
So if I understood well, information is coded as 7 times 23406 vertices (which in total makes the 163842 vertices corresponding to my average surface), and for each vertex I have 6 values.
I have thus two questions on beta.mgh:
- The first two values look like thickness measurements, and thus
may be the average thickness for group 1 and group 2, is it right?
Yes, the first should be thickness for group 1 and the 2nd for group 2.
- Can I also ask you what are the 4 other values?
Those would be the slopes for the continuous variables you defined in the fsgd file.
doug
Thank you very much for your help,
Marie Schaer
On Feb 9, 2007, at 7:22 PM, Doug Greve wrote:
If you are going to run mri_glmfit on the thicknesses in order to do stats, then this should/could be one of the outputs. If you make two groups in the fsgd file, then the first frame of the beta.mgh file will be the average thickness for group1, and the 2nd frame will be group 2.
use something like:
mri_convert beta.mgh group1.mgh --frame 0 mri_convert beta.mgh group2.mgh --frame 1 doug
Marie Schaer wrote:
Hello,
I have a two groups comparison design, and I was wondering if there is any easy way to compute an average thickness file per group (in order to be able to overlay mean thickness values on my average subject). Is there an existing command or matlab function to do it? If yes, would I also be able to do a standard deviation file using the same command?
Many thanks,
Marie Schaer _______________________________________________ Freesurfer mailing list 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 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 -
Marie Schaer