it's only positive for the contrast that you have specified. the roi summary reports the HRF amplitudes for each condition. When you compute the contrast of those, you should get the right sign.

doug

Dave Brohawn wrote:

Hello,

In the stable 3 environment, I ran the func2roi-sess command. This is what was included:

func2roi-sess -roidef dACC99_rh -analysis EMerror -anatlabel dACC-rh -maskcontrast ASevfix -maskframe 5 -maskthresh 0.0043648054 -masktail pos -maskmap sig -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR

I then ran this summary generating command:

roisummary-sess -roidef dACC99_rh -analysis EMerror -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR -sumfile $SUBJECTS_DIR/dACC999_rh.txt

I've viewed the summary file, and found that there are negative values listed for some of the conditions time points (e.g conditon 1, 2 sec after stimulus onset).

How can this be if I included the masktail pos flag? I thought that only captured positive activation.

If there is a way to solve this issue and capture only positive activation, please post when you can.

Thank you,

Dave Brohawn _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer