Hello, MRtrix support team,
I am working with MRtrix to get a structural connectome based on data that was provided for me by some professionals. What I need is the mean length of fibers between 85 ROIs and the mean number of fibers between them, for which I use the following commands respectively:
tck2connectome -symmetric -zero_diagonal wb.tck parcellation.mif -stat_edge sum number.csv tck2connectome -symmetric -zero_diagonal wb.tck parcellation.mif -stat_edge mean -scale_length length.csv
My very first question is whether these commands would work for my intention?
Secondly, the results I got from these two commands had a bit of a problem, compared with literature, my numbers were off. My maximum mean number of fibers was a thousand times bigger and the minimum mean length of the fibers six times smaller than the respective values in the literature. I know that working with just one brain, the numbers might slightly differ from working with mean values form many brains but my numbers are orders of magnitudes larger. My question is can you help me find what might be the underlying cause of this problem?
I tried to understand why this phenomenon happened by going one step back and generate my own tractography, I limited the minimum length of the fibers to 10 mm and I found out a region is losing all it’s connections, the temporal pole. I lowered the limit step by step until at 3 mm minimum I got the connection in that region back. The problem is the distance between the center of the mass of this region and the connected regions at this minimum (obtained by mrcenter code I found on this forum) is between 11 to 45 mm and the length of the streamline I get is around 4-5mm. I am wondering why this is happening?
The command I’m using to get my tractography is:
tckgen fod.mif wb_mn3mx130.tck -act aparc+aseg_5tt_al.nii -seeds 5M -minlength 3 -maxlength 130 -seed_gmwmi gmwmi_5tt_al.nii
I am very confused and I’m not sure what should I do next.
Thank you in advance