I am trying to do an along the track analysis, and have come across issues.
I have a CST track (full_CST.tck below) with max 7500 streamlines. Originally generated using include ROIs at the cerebral peduncle (CP) and posterior limb of the internal capsule (PLIC).
I am analyzing stroke brains with varying CST lengths, so decided to create a generic start point and create cuts along the tract at the same distance (2mm).
Using tckedit, I have cut the track shorter (cut_CST.tck).
I used a whole brain mask cut at the level of the CPs (to generate the shorter track), with an include ROI at the PLIC (PLIC.mif).
Next, I ran tckresample to cut at every 2mm, then ran tcksample to extract FA values from each segment.
A couple of issues:
- The cut track is visually shorter (mask worked), but has more segments than the original (8627).
- minlength was set to 40. Yet the cut_CST.tck minimum from tckstats is 0.117562. This distance also wouldn’t reach the -include ROI of PLIC.mif.
- The txt file outputted from tcksample included data for 61 cuts, yet tckstats indicated the longest streamline was 112.861 (/2=56 cuts maximum).
Any insights into why this is happening and how I can fix it would be ++ appreciated.
tckstats full_CST.tck tckstats: [100%] Reading track file mean median std. dev. min max count 107.391 108.511 7.86463 58.7816 117.563 7500 tckedit -mask CPmask.mif -include PLIC.mif full_CST.tck cut_CST.tck -nthreads 0 -number 7500 -minlength 40 tckedit: [done] 7500 read, 7500 written, 8627 segments tckstats cut_CST.tck mean median std. dev. min max count 76.4346 86.7616 28.065 0.117562 112.861 8627 tckresample -step_size 2 cut_CST.tck cut_CST_2mmseg.tck tcksample cut_CST_2mmseg.tck famap.mif cut_CST_2mmseg_fa.txt