[Mrtrix-discussion] MRstats Specific to the Corticospinal Tract

[Kirles Bishay]

Hello,

I am currently trying to get statistics specifically on the corticospinal
tract of my whole brain TDI images. So far, I have tried to create a mask
of just the CST to apply to the whole brain image by using the tractography
function in MRtrix, turning it into a TDI image, using ImageJ software
to convert the TDI image into a mask and then applying the mask back
in MRtrix to specify my ROI for the statistics function. While this works
well with the TDI image of just the CST, it does not work with the whole
brain image because the dimensions of the images are different. This is
because the dimensions created with my ROI tractography differ from the
dimensions of the whole brain tractography. I have tried to change the
dimensions of my mask image using ImageJ, but I think this warps the mask
inapropriately. Is there a way to control the output dimensions of the
tractography images so that I can match the CST mask to my TDI image? Or do
you have any other suggestions to get the data on the CST in my whole brain
images that I have not thought of?

Thank you,

Kirles
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