I am having trouble using Slicer to view a directionally-encoded color track density imaging (DEC-TDI) map created in MRtrix (documentation: https://mrtrix.readthedocs.io/en/latest/reference/commands/tckmap.html). The volume displays in color in MRtrix, but displays in grayscale in Slicer. In order to compare to a DEC-FA map that correctly displays in color in Slicer, I am trying to determine how I can alter the MRtrix file to display in color in Slicer.
The two DEC files (FA and TDI maps) can be found in this Dropbox folder: https://www.dropbox.com/sh/5vw4bexypqyxr1r/AAATxL0pLsoU2jyLbTeGh3Pla?dl=0
“Subject1_FA_DEC.nii” is the file that displays in color in Slicer.
“Subject1_TDI_DEC.nii.gz” is the MRtrix-generated file that displays in grayscale in Slicer (want color).
From the Volumes module, we see that,
Scalar type: unsigned char
Volume type: vector
Subject 1_TDI_DEC.nii.gz has:
Scalar type: float
Volume type: scalar
From the NIFTI headers, we see that,
Subject1_FA_DEC.nii has image dimensions: [112×112×60×3 uint8]
Subject1_TDI_DEC.nii.gz has image dimensions:
From this information, we believe that Slicer may only be reading one component of the three-component MRtrix data, thus resulting in grayscale, and not color, display.
If anyone else has encountered this problem, or something similar, please let me know.
Thanks in advance.