I am opening this topic because I couldn’t find a satisfactory answer to my question. I have used IFOD and generated probabilistic tractography on a stroke sample. The stroke is in the left hemisphere (where no tracts are expected).
I tried to visualize the tractography using tckedit. I gave it either 2million or 5million streamlines to show.
In certain slices, there are no streamlines seen in the right hemisphere where the cursor is. Is this because of the downsampled number of streamlines or due to any other issue? I checked the WM segmentation and it looks fine. Also, I created a TDI file over the original bigger .tck file and it doesn’t show a tract in the approximate voxel location
I am attaching three different subjects who I saw this happening in.
Could you please advise?
Thank you in advance.
There’s a bunch of different mechanisms that could be leading to an absence of streamlines in a given location, and so it requires a bit of experimentation to isolate before you can consider what you might change about the pipeline to remedy it.
Are you using a propagation mask, and those areas are excluded from that mask?
Are you using ACT, and the tissue segmentations in those areas are inappropriate?
Are the FOD amplitudes in those regions lower than the propagation threshold?
Is the correction of susceptibility distortions inappropriate in those regions?
(moreso examples 2 and 3 rather than 1)
One other trick you can try is provide
tckgen with a seed image corresponding to the region where you expect to get streamlines but aren’t, and include the
-info flag. It will give a bunch of statistics about why streamlines were terminated, and why they were rejected from being written to the output file.
Thank you so much for these suggestions. I will troubleshoot my data using these points.
This is very helpful!
Thank you so much