Hi Adam, use the "paired" method in the fsgd examples. doug On 06/29/2012 11:58 AM, 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 > niten...@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 > >
-- 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 _______________________________________________ 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.
