MRTrix vs. Slicer color information

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1

Hello,

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,
Subject1_FA_DEC.nii has:
Scalars: 3
Scalar type: unsigned char
Volume type: vector
Subject 1_TDI_DEC.nii.gz has:
Scalars: 1
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:
[448×448×240×3 single]

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.

2

We followed up on this off-list, here’s a way to get it working:

One needs to pip_install("nibabel"). Then the key lines are:

b = "/home/pieper/Downloads/AG2003_CSD_TDI_5_dec_b0.nii.gz"
ii = nibabel.load(b)
slicer.util.addVolumeFromArray(ii.get_data(), nodeClassName="vtkMRMLVectorVolumeNode")

image
image819×563 116 KB

I also manually edited the space directions so the volume was roughly oriented correctly, but it may still be left-right flipped.

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