Fiber tracts between a seed and target regions

1

Hi experts,
I just wanted to do the fiber tracking between a seed region and a target region. Below is the command line that I used.
tckgen
-algorithm Tensor_Det
/dti/results_mrtrix/data.nii.gz
track.tck
-fslgrad /dti/results_mrtrix/bvecs /dti/results_mrtrix/bvals
-mask /dti/results_mrtrix/nodif_brain_mask.nii.gz
-angle 45
-minlength 20
-maxlength 250
-rk4
-cutoff 0.15
-step 0.5
-seed_image /dti/results_mrtrix/seed.nii
-include /dti/results_mrtrix/target.nii

It run smoothly, however, when I use mrview to visualize the track.tck, it showed
mrview: [ERROR] unknown format for image “track.tck”
mrview: [ERROR] error opening image “track.tck”

Do you have any thoughts about this error?

Best,
Cain

2

Hello Cain!

When you attempted to visualise track.tck, did you load it into mrview as the main image (e.g. something like mrview track.tck? mrview requires a main image to be loaded (e.g. of type .nii.gz or .mif), and then you can visualise the tractogram on top of that image. To visualise tractography files you need to load them using the -tractography.load track.tck option (or use the tractography tool in the GUI). You can still hide the background image using -imagevisible 0 if you prefer. Does that help?

Fiona

3

OK, great. Thanks for your help. Problem solved.