How to convert tck file to binary nii.gz

Hi all

I am trying to convert tract files (tck) to binary files. I was instructed to use flsmaths - bin option to do that but I suspect that it doesn’t work with tck files as I keep getting errors that my file does not exist (I checked and all the paths are correct).

I found tckmap which worked but it didn’t create a binary file.

Does anyone know an easy way to make a conversion from tck to binary image?

Many thanks


Hi Vasilis,
In case you successfully generated an image volume of the tck using tckmap, you should be able to use mrtrix (mrtreshold) or fsl tools (fslmaths) to make a binary image of the image created by tckmap


It is also possible to feed the output of tckmap into mrcalc to generate a binary image, for example

mrcalc <tckmap_output> 0 -gt <binary_tck.mif>

Hope this helps!