Hi everyone,
I was hoping I can get some clarification on two things.
First is: I was taking a look at the output “PAIRMAP” after running 3dtrackID -mode prob
and I noticed that the tracts are not necessarily continuous and connected between a pair of ROI’s.
I’ve attached an image of what I mean. Is this normal? I thought the way probabilistic tractography works is that it only include a single path (the more likely path) and does not include any paths that may deviate away from that and end at a random spot.
Second: Also, can I get the connectivity values between pairs of ROIs (from probabilistic tractography)? Which file is that? I tried to open the file ending in “PAIRMAP.niml.lt” but that doesn’t seem to be the correct file. I’m only asking so I can perform statistical analysis on it.
Any help would be appreciated.
Hi, Sondos-
Output text files of properties are “*.grid” files; please search for “grid” in the 3dTrackID help file for more information, and also in this online documentation for more description:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/FATCAT/Tracking.html#outputs-common-to-all-modes
For more information on the tracking functions and how they work, please see this documentation:
https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/FATCAT_03_dti_tracking_funcs.pdf
For probabilistic tracking “WM ROIs” or “WM connections (WMCs)” need not be contiguous.
What determines whether a voxel is “in” a WMC between a given pair of targets (say, A and B) is purely: is the number of tracts between A and B that run through the voxel greater than the threshold value? Each voxel is tested independently according to that criterion. It is possible that WM ROIs can be “patchy”.
Note that I don’t htink looking at the PAIRMAP is as informative as looking at the set of individual connections, as described here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/fatcat_prep/Postprocessing_IV.html
since in the PAIRMAP file, there is less specificity, in general.
–pt
