How to convert tck file to binary nii.gz

1

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

Vasilis

2

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

cheers
William

3

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!

Cheers,
Arkiev