Hi FreeSurfer experts,
I recently ran a simple fMRI analysis in FSL and now generating images of the activation in freesurfer using reg-feat2anat to register the functional activation to the freesurfer recon-all files, and generating the images using tksurfer:
tksurfer pilot_3 lh inflated -annot aparc.annot -ov run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat -fthresh 4 -fslope 1
However I have come across a strange occurrence when I change the threshold. Specifically, when I set the -fthresh flag (bolded) as 4 (i.e. p=0.0001) or less, the activation colors comes off as they should (see 4_blue attached) in terms of how I set up the contrasts. But when I set my threshold to 5 or higher (changing nothing else), the colors of the activation invert (see 5_red attached).
What does this mean? How can I fix this?
Any ideas would be greatly appreciated!
Thank you! Gabriella
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