Hi Adam,

if you use the longitudinal stream for it (it is designed for that stuff and will increase reliability), you will have the surfaces in the same space and can simply subtract the thickness files (mris_calc) and visualize on any one of them.

Best, Martin

On Fri, 2012-06-29 at 11:58 -0400, Adam Nitenson wrote:

Hi all,

I am trying to visualize the surface map showing the Post Treatment - Pre Treatment cortical thickness in a single subject. The Post and Pre scans are processed like 2 separate subjects.

I used the commands:

mris_preproc --f /cluster/roffman/users/Stable5_PerRun/Subject_Files/FB12_Pairs/FB0011040 --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/FB12_Pairs/FB0011040/THICKNESS-MAP-LH.mgh

and

mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/FB12_Pairs/FB0011040/THICKNESS-MAP-LH.mgh --fsgd /cluster/roffman/users/fsgd/FB12_Pairs/FB0011040.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/FB12_Pairs/FB0011040/Post_Minus_Pre/LH --surf fsaverage lh --fwhm 4.6

The subject and fsgd lists only have 2 subjects (the post and the pre) and the contrast is the 1 -1, same as the group.diff.mtx on the Wiki.

I receive the error DOF = 0, which is likely because each group only has 1 subject. Usually I have multiple subjects in each group. Is there an alterate way to generate this difference map when only using 2 subjects??

Best,

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson@nmr.mgh.harvard.edu Phone: 617-643-3215 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer