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 > > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
