tckmap output nifti values

Hi MRtrix3 folks. This may be a simple question but I cannot seem to find the answer anywhere. When tckmap is used to convert a track file (such as a .tck) file to a nifti, the nifti file output by this process contains a numerical value in each voxel. What do these values mean? Are they representative of some track value, such as directionality? Or do they represent something else entirely?

Hi - assuming you’re using tckmap defaults, perhaps take a look at the default settings under the -contrast and -stat_vox flags on the tckmap documentation. tckmap has several options that allow you to control the mapping of tck to the scalar image.

Feel free to provide more specifics on what you’re trying to do (e.g., do you have a tract of interest in *.tck and an FA metric map in *.nii.gz and you’re trying to get mean FA in the tract?).

Thank you so much for the reply!

That is exactly what I’m trying to do. I am trying to use a .tck converted to a .nii in an ROI analysis. One of the options I’m considering at the moment is eroding the .nii to eliminate partial volume effects influencing the mean metric value. It would be easy to do this by simply thresholding out certain intensity values in the .nii. But, of course, I need to know what those intensity values actually represent.

The -contrast and -stat_vox flags look like what I may need here.

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