Hi everyone, I`m doing some tests with tractography options in tckgen.
First, I used the -select and it worked OK, I used the command below.
tckgen -algorithm iFOD2 -select 100000 -cutoff 0.05 -step 1 -angle 45 -minlength 50 -maxlength 200 FOD.mif test_select100000.tck -seed_image seed_ROI.nii -include target_ROI_gmwmi.nii -crop_at_gmwmi -act 5TTimage_freesurfer.mif
Then, I was able to get the following results.
2966512 seeds, 2652680 streamlines, 100000 selected
Second, I used the -seeds, I used the command below.
tckgen -algorithm iFOD2 -seeds 3000000 -select 0 -cutoff 0.05 -step 1 -angle 45 -minlength 50 -maxlength 200 FOD.mif test_select100000.tck -seed_image seed_ROI.nii -include target_ROI_gmwmi.nii -crop_at_gmwmi -act 5TTimage_freesurfer.mif
Then, the results
3000000 seeds, 2683622 streamlines, 100539 selected
I have doubts about this results.
I understood that if ‘-select’ is set to zero, it will be disable. But, final results show the number of selected streamlines. I checked number of tracks through ‘count’ option in tckinfo, same this too.
And I have one more question.
It seems that many people usually use ‘-select’, when they extract tractography. So, when do I use ‘-seeds’?
And I want to finally get fiber density and proceed with the intersubject analysis. In this case, which option should I use, ‘-select’ or ‘-seeds’?