Missing fibres

I am going to extract Corpus Callosum fibers. After following the initial steps, I used “tckgen” command and chose my saved ROI (which was segmented by fsl) as a seed_image :

tckgen fod.mif CC.tck -seed_image CC_dti_corrected.nii.gz -mask mask.mif -select 3000 -cutoff 0.15 -force

The problem is the extracted fibers are not complete. You can see the result in the attached file. I check my ROI and fiber orientation distribution file. They look both alright. I have used this method for multiple subjects and a few of them had this issue, most of them were alright.

Could you please help me with this problem?


Hi Maryam,

When conducting CC tractography, it is often important to make the mask (from sagittal) more than just 1 (mid-sagittal) slice. That is, I usually do 3 sagittal slices: 1 from mid-sagittal, and then 1 from the both sides as well. If you only do 1 slice (mid-sagittal), then you usually get everything but the isthmus (which I think is what happened in the example you uploaded). Sometimes you will also get crossing fibres (which extend inferiorly in the corticospinal tract; CST) so you may need to place small exclusion masks to ensure they are not tracked. You will know when you have tracked the CC properly as you will also see the tapetum (1 on each side).

And/or try reducing the FA threshold (i.e. reducing the -cutoff value).



Hi Jerome,
Thanks for your reply. I segmented the whole corpus callosum using the standard mask by FSL. So it is not just one mid-sagittal slice. I tried changing the cutoff value and also the number of fibers, then I got a better result. But the point is because I want to extract CC for multiple subjects and do some statistics test on them, I wanted all the parameters for extracting the fibers to be the same. I do not know how much it is important and if I set different cutoff values, does it affect my final result or not. Because for the 10 subjects I’ve done so far, just 2 had this problem and others showed all CC fibers properly.