I would like to use the output of TORTOISE into a FreeSurfer tool called AnatomiCuts to cluster white matter streamlines. The main inputs are a streamline file in .vtk format, and a .nii segmentation file. I have two questions regarded to the creation of these files.
1) I know from the GUI export menu that .vtk is natively supported by TORTOISE. However, I would like to keep the whole process in the command line. Is there a way to script this kind of export?
2) Does TORTOISE at any point output a brain map segmentation file (xxx_parc.nii.gz for example)?
Unfortunately we do not have any export command to VTK at the moment.
You can use another tractography software that can output a trk file or vtk file, trackvis can do it.
No we do not output any segmentation maps either. The outputs of tortoise can be used for that purpose in freesufer but generally a T1W anatomical image is required.
Hope this helps.