On 01/16/2014 11:57 AM, Danielle Miller wrote:
Hi Freesurfer Experts,
I have some questions regarding mri_glmfit - some basic and some not so basic - that I hope you can help me with.
1.) I want to do a thickness analysis looking at the effect of a continuous variable on thickness while regressing out effects of both continuous and categorical variables. Let's just say I have one continuous variable of interest, one to regress out, and one categorical variable (with four groups) to regress out. From reading other posts, it seems that I should make my categorical variables into a class - if I do this will this contrast look at the effect of my continuous variable while regressing out effects from the other variables (including group)? This is assuming I am running a DOSS analysis 0 0 0 0 0 1
Yes, that is correct.
2.) In the cluster corrected significant image, I am a bit confused on what the positive and negative significance values represent. If I was looking at group differences - would red indicate that the first group
second group, and blue indicate first group < second group (that is,
first group with increased or decreased thickness compared to second group)?
Yes
3.) Lastly, I see that you can use mris_preproc and glmfit to look at volume. Does this look at volume in a voxel-based way? That is, is it comparing volume on a voxel level? If so, would the correct commands be: mris_preproc --fsgd FSGD FILE --target fsaverage --hemi lh --meas volume --out OUT.mgh mri_glmfit --y MGH FILE --fsgd FSGD FILE doss --C CONTRAST --surf fsaverage lh --glmdir GLM DIR Would I need to smooth the data?
It does look at volume in a voxel/vertex specific way. I would certainly smooth the data. The command looks right. doug
Thanks for any and all help! Danielle
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