Hi Tracula Experts,
How do you determine if a pathway reconstructed well? I've been examining the merged pathways (<subj>/dpath/merged_avg33_mni_bbr.mgz) in freeview, and if the pathway looked too small when viewing with the default threshold, I would reinitialize those pathways. Most of the time, the new pathway would look ok upon re-inspection. A few pathways, however, still appear too small when viewed at the default threshold in Freeview, but at lower thresholds, they begin to look ok.
I've encountered 1 pathway that still appears too small in Freeview, but the output in pathstats.overall.txt and pathstats.byvoxel.txt seem reasonable. On the other hand, its path distribution (path.pd.nii.gz) does not look like a distribution, but a single path -- there are a 38 voxels with values of 4000, and all others are 0. This doesn't seem right. What could cause this to happen?
What objective measure can I use to determine if a pathway is reconstructed well enough?
Thanks, Peggy