Hi all,
I want to use the --prv (per vertex regressors) option in mri_glmfit, but there is very little information in the Wiki and I couldn't find any relevant info in the mailing list.
I have two .mgz files, one contains the dependent variable, the other is the source of my pvr. I tried loading one column from the second file and appending it to the design matrix in Matlab for each vertex (in a loop), but it's too time consuming to be feasible. Someone tipped me about the pvr option in mri_glmfit but from the Wiki (see below) it seems I would have to load the regressors individually here as well..?
What is pvr1, pvr2 etc. in the example below? Text files? That's either going to be one very long command line or I have to use a loop here too (probably in Matlab). Is there any way to tell mri_glmfit. "for each vertex in the dependent variable file, take the corresponding vector from the pvr-file and append it to the design matrix"?
[from the WIki:]
--pvr pvr1 <--prv pvr2 ...>
Per-voxel (or vertex) regressors (PVR). Normally, the design matrix is 'global', ie, the same matrix is used at each voxel. This option allows the user to specify voxel-specific regressors to append to the design matrix. Note: the contrast matrices must include columns for these components.
Thank you!
Hi Lars, the way it works is that each pvr that you spec on the cmd line indicates another column in the design matrix. If you want multiple columns then add multiple --pvr options (thus pvr1, pvr2, etc). If you do not spec an X matrix or fsgd file, then it will assume that you want a column of 1s at each vertex. You need to create contrast matrices that have enough columns to cover all the columns in the design matrix, both fixed/global and per-vertex.
doug
On 12/12/2012 04:43 AM, Lars M. Rimol wrote:
Hi all,
I want to use the --prv (per vertex regressors) option in mri_glmfit, but there is very little information in the Wiki and I couldn't find any relevant info in the mailing list.
I have two .mgz files, one contains the dependent variable, the other is the source of my pvr. I tried loading one column from the second file and appending it to the design matrix in Matlab for each vertex (in a loop), but it's too time consuming to be feasible. Someone tipped me about the pvr option in mri_glmfit but from the Wiki (see below) it seems I would have to load the regressors individually here as well..?
What is pvr1, pvr2 etc. in the example below? Text files? That's either going to be one very long command line or I have to use a loop here too (probably in Matlab). Is there any way to tell mri_glmfit. "for each vertex in the dependent variable file, take the corresponding vector from the pvr-file and append it to the design matrix"?
[from the WIki:]
--pvr pvr1 <--prv pvr2 ...>
Per-voxel (or vertex) regressors (PVR). Normally, the design matrix is 'global', ie, the same matrix is used at each voxel. This option allows the user to specify voxel-specific regressors to append to the design matrix. Note: the contrast matrices must include columns for these components.
Thank you!
-- yours,
Lars M. Rimol, PhD Division of Mental Health and Addiction Institute of Clinical Medicine University of Oslo P.O. Box 85 Vinderen, 0319 Oslo, Norway
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-
Douglas N Greve -
Lars M. Rimol