Dear FreeSurfer Group,
I have a brief question about how thresholding is conducted in TRACULA. I am looking to threshold path.pd.nii.gz for use as a mask in other analyses. However, I am having difficulty determining the threshold to use to create an appropriate mask. The FreeSurfer literature and wiki suggest that the optimal threshold is 20% of the maximum value. However, this differs from the apparent thresholding used to create the merged_avg file and pathstats.overall.txt.
For example, when I load my merged_avg into freeview, the automatic threshold for the forceps major for a given subject is 39.4, and when I threshold path.pd.nii.gz at 39.4, the volume is 679 voxels. This volume matches the volume seen in pathstats.overall.txt. Given that 20% of the maximum is 39.4, I should expect the maximum threshold to have an intensity of 197. However, the maximum threshold is 509, making 39.4 only 7.74% of the maximum value. This suggests that I should threshold path.pd.nii.gz at 101.8. While I used the forceps major as an example, this issue persists across tracts and across subjects. There doesn't appear to be any clear pattern which suggests the tracts are thresholded at a consistent value for all tracts; for one subject, the reported 20% of max is in actuality anywhere from 6.43% to 15.11% of the actual maximum value. I also attempted to force dmri_mergepaths to give me the appropriate maximum value by running the command with a --thresh value of 1. However, the output still opened in freeview with a reported maximum intensity of 197. I am using tracula in FreeSurfer 6.0.
How does TRACULA conduct its thresholding within dmri_mergepaths and dmri_pathstats? Why does there appear to be a discrepancy between the reported maximum value and the actual maximum value? And what threshold should I use to create my mask for use outside of FreeSurfer? Thank you for your help.
Best, Duncan Cleveland University of Minnesota