Def. sounds worth doing then! I'll give it a try. My other question is, where can I get my hands on the average7? It's used as the target in the mris_glm examples, but I haven't been able to find the actual average7 surface in any of the freesurfer directories. Am I missing something? Thanks again, Alex
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tuesday, June 21, 2005 4:11 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_glm
You can run with just the design matrix, but you won't be able to use the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a way to specify how to build the des mtx. The fsgdf keeps track of what the regressors mean (eg, Age, Class, IQ, etc). When you save the preprocessed data with --y, you'll see that there will be an fsgdf file saved with it. Load this in tksurfer, click on a point, and you will be able to make a scatter plot of, say, thickness vs age, with each class (eg, Male, Female) having a different color dot in the scatter plot. When you mouse-over the dot, it tells you the subject name. Click on a new point and you'll see the scatter plot for that point. If you use --xmat, you can save the design matrix (in matlab-4 format).
doug
On Tue, 21 Jun 2005, Fornito, Alexander wrote:
Hi,
I was seeking some clarification re: the relationship between the
fsgdf
and design matrix file for use with mris_glm. It seems to me that the two contain very similar info, the examples in the -help don't use the fsdf at all. Is it necessary to create one, or can you just run an analysis with the desmtx?
Thanks,
Alex
Alexander Fornito
M.psych (Clin. Neuro.)/PhD candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
alexander.fornito@wh.org.au
Hi Alex,
you're better off using the make_average_surfaces.csh script to make an average of your subjects. Nick: can you send Alex a copy?
thanks, Bruce On Tue, 21 Jun 2005, Fornito, Alexander wrote:
Def. sounds worth doing then! I'll give it a try. My other question is, where can I get my hands on the average7? It's used as the target in the mris_glm examples, but I haven't been able to find the actual average7 surface in any of the freesurfer directories. Am I missing something? Thanks again, Alex
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tuesday, June 21, 2005 4:11 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_glm
You can run with just the design matrix, but you won't be able to use the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a way to specify how to build the des mtx. The fsgdf keeps track of what the regressors mean (eg, Age, Class, IQ, etc). When you save the preprocessed data with --y, you'll see that there will be an fsgdf file saved with it. Load this in tksurfer, click on a point, and you will be able to make a scatter plot of, say, thickness vs age, with each class (eg, Male, Female) having a different color dot in the scatter plot. When you mouse-over the dot, it tells you the subject name. Click on a new point and you'll see the scatter plot for that point. If you use --xmat, you can save the design matrix (in matlab-4 format).
doug
On Tue, 21 Jun 2005, Fornito, Alexander wrote:
Hi,
I was seeking some clarification re: the relationship between the
fsgdf
and design matrix file for use with mris_glm. It seems to me that the two contain very similar info, the examples in the -help don't use the fsdf at all. Is it necessary to create one, or can you just run an analysis with the desmtx?
Thanks,
Alex
Alexander Fornito
M.psych (Clin. Neuro.)/PhD candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
alexander.fornito@wh.org.au
Alex,
Attached is the make_average_surface script. Copy it to the freesurfer/bin directory, and be sure to make it executable (run 'chmod 755 make_average_surface' in the freesurfer/bin directory).
Type 'make_average_surface' to get help. Basically, just the subject names are required. By default, a 'subject' named 'average' will be created from your set of subjects (a name instead of 'average' can be specified on the command line).
Nick
ps. I am working on the mris_surface seg-fault problem using the rh.orig file that you sent.
On Tue, 2005-06-21 at 08:23 -0400, Bruce Fischl wrote:
Hi Alex,
you're better off using the make_average_surfaces.csh script to make an average of your subjects. Nick: can you send Alex a copy?
thanks, Bruce On Tue, 21 Jun 2005, Fornito, Alexander wrote:
Def. sounds worth doing then! I'll give it a try. My other question is, where can I get my hands on the average7? It's used as the target in the mris_glm examples, but I haven't been able to find the actual average7 surface in any of the freesurfer directories. Am I missing something? Thanks again, Alex
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tuesday, June 21, 2005 4:11 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_glm
You can run with just the design matrix, but you won't be able to use the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a way to specify how to build the des mtx. The fsgdf keeps track of what the regressors mean (eg, Age, Class, IQ, etc). When you save the preprocessed data with --y, you'll see that there will be an fsgdf file saved with it. Load this in tksurfer, click on a point, and you will be able to make a scatter plot of, say, thickness vs age, with each class (eg, Male, Female) having a different color dot in the scatter plot. When you mouse-over the dot, it tells you the subject name. Click on a new point and you'll see the scatter plot for that point. If you use --xmat, you can save the design matrix (in matlab-4 format).
doug
On Tue, 21 Jun 2005, Fornito, Alexander wrote:
Hi,
I was seeking some clarification re: the relationship between the
fsgdf
and design matrix file for use with mris_glm. It seems to me that the two contain very similar info, the examples in the -help don't use the fsdf at all. Is it necessary to create one, or can you just run an analysis with the desmtx?
Thanks,
Alex
Alexander Fornito
M.psych (Clin. Neuro.)/PhD candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
alexander.fornito@wh.org.au
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