How to add two .tck files of one subject together

Dear experts,
I had got two .tck files through tckgen. The only difference between these two .tck files was one with “-include bithalamus.mif” and another with “-exclude bithalamus.mif”. Now I want to combine these two files and divide it by bithalamus ROI obtained from other method.
By the way, is there any flaw in the above-mentioned method or recommendation for me which method to better segment the thalamus based on T1 and T2 image?
I noted that the thalamus on vis.mif was smaller than that from FSL’s FIRST.
Thank you very much!

Hi ZhangHui,
I can answer your first question: to merge two .tck files you can do

tckedit file1.tck file2.tck merged_tracks.tck

The created file merged_tracks.tck should then contain the streamlines of both input files.
Not sure about the second part of your question about dividing that by a ROI…

Kr,
Thibo

Ha, it works. Thank you very much! Looking forward to replies to other questions.

Hi Zhang,

The only difference between these two .tck files was one with “-include bithalamus.mif” and another with “-exclude bithalamus.mif”. Now I want to combine these two files and divide it by bithalamus ROI obtained from other method.

I think you need to refine your explanation here before we can get to an answer: the intended operation that you are referring to as “divide” is unclear, particularly as it seems to be in reference to both streamlines and image-based data.

I noted that the thalamus on vis.mif was smaller than that from FSL’s FIRST.

Assuming that you used 5ttgen fsl, the thalami in the 5TT image (and consequently the 3D visualisation version of such) is itself calculated using FSL FIRST. The difference is that the generation of the 5TT image directly computes partial volume fractions for those voxels intersecting the surface (as shown in the ACT manuscript), whereas the binary images exported directly from FIRST include all voxels that are detected as having any intersection with the surface. So personally I consider the latter to be an over-estimate; in cases where a binary mask is required, I prefer to threshold the partial volume image at 0.5.

Rob

Hi Rob,
Happy to hear from you and thanks a lot!

Hui