Hi Clark, mri_glmfit should work fine. If you have the ROIs in a volume format (eg, nifti or mgh) you can run mri_concat on them to create a stack, then just pass the stack to mri_glmfit with the --y flag (also add --no-est-fwhm). If you don't have them in a volume format, you can create a volume format in matlab, something like

mri.vol = load('yourdata.dat'); mri.vol = vol(:)'; % make sure each ROI is in a different column instead of row MRIwrite(mri,'youdata.nii');

doug

On 11/22/13 5:51 PM, Clark Fisher wrote:

Hi Freesurfers,

I am working with fsfast, and interested in doing a 2nd-level fixed effects analysis over a number of subjects. However, the volumes I'm using aren't in a standard freesurfer space (native, talraich, etc.). They are nx1x1 volumes containing results from n ROIs. While I got first level analysis in fs-fast working, I don't think I'll get mri_glmfit to work in this space.

What is the math that mri_glmfit carries out to do the fixed-effects analysis? Based on the inputs, it seems to rely upon the variance and degrees of freedom from each individual subject, and I can't find a formula in the general MRI literature (or in the freesurfer group analysis presentation) that uses both of these in a fixed-effects analysis.

Thanks, Clark _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer