Convert tck/nifti to dicom without losing color coding

[Bhagyasree-knauparthi]

Dear Karawun Team,

I am converting the tract (tck) files to dicom in order to allow the viewer flexibility and choice. In this process I converted tck to nifti and then to dicom. When I checked, both tck and nifti files have the color doing (directions of fibers) in it. In the same way, I need color-coded dicom files. I've tried a couple other options for converting nifti to dicom, but I can't seem to keep the colour coding. Please let me know if there is any possibility of conversion directly from tck to dicom, or any other ways without losing color coding in the final dicom files.

Thanks

[richardbeare]

Hi, Thanks for trying Karawun. Do not convert the tck files to nifti. Leave them as tck and include them on the command line as part of the --tract-files argument. See example below from the doc page. Karawun does not create colour dicom in the traditional per-voxel sense. Colour is assigned to segmentation format dicoms created via either the --tract-files or --label-files arguments.

importTractography --dicom-template path/to/a/dicom --nifti T1.nii.gz fa.nii.gz --tract-files left_cst.tck right_cst.tck --output-dir path/to/output/folder