Try changing the thresholds (via the Configure button). When it first loads, the thresholds are set very low. When they get changed to your values (4,5), then there is nothing left and it looks like a blank brain.

On 7/6/2019 9:38 AM, Marie Hill wrote:

External Email - Use Caution

Hi everyone,

I have just finished running glmfit. When I try to load the significance maps in freeview, they appear to load for a moment and then disappear, just showing the brain volume without any highlighted areas of significance. Does anyone have any idea why this could be?

I ran the command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.g4v1.glmdir/bipolar-vs-schizophrenia/sig.mgh:overlay_threshold=4,5 -viewport 3d

Kindest Regards,

Marie

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