Thank you Nic for your reply.
I’ve decided to use the lesion volume, but I have a couple of questions concerning the results.
Below you can see the results from a subject with a huge WMH lesion load (I’m working with 7T data, so the WMH burden detected on FLAIR and T1 can be higher than at lower field strength). I generated 10 million streamlines and in the figure below, 5 million of them are rendered (the opacity of streamlines is set to 0.3). The picture is showing the fifth volume with the WMH mask and the streamlines.
Some tracts are not passing through the lesion, but in other portion they are passing trough and/or terminating in the lesion. I’m wondering if this can be an expected and acceptable behavior when using the lesion volume, or if I still need to refine my processing steps for this point. What do you think?
I am new to the tractography world, but I would expect streamlines to pass, enter, exit (5ttgen: Recommended approach to dealing with white matter hyperintensities (WMHs) for ACT - #2 by cbajada) all over the lesions, not just in some portions. Maybe, this information is in the 5 million streamlines that I cannot render (my graphic card is “only” 4 GB so I cannot render all the 10 million) or more simply 10 million are not enough streamlines to “cover” everything and I should push the number to let’s say 30-40 millions (or even more, I saw that sometimes also 100M is suggested?)
Thank you in advance for any clarification and suggestion.
Before the picture, I copy and paste the commands I’m using the generate and render the streamlines:
tckgen wmfod_norm.mif tracks_10mio_final.tck -act T1w_5tt_WMHlesion_coreg.mif
-seed_gmwmi gmwmSeed_coreg.mif -backtrack -select 10M -maxlength 250
-minlength 5 -cutoff 0.06 -crop_at_gmwmi -nthreads 8 -debug -force
tckedit tracks_10mio_final.tck -number 5M tracks_5M_from10M.tck -force
mrview T1w_5tt_WMHlesion_coreg.mif -overlay.colourmap 2 -tractography.load \ tracks_5M_from10M.tck -tractography.opacity 0.3 -mode 2
Best,
Riccardo