Now I’m using tensor2metric for making the FA, ADC, RD map.
Before running tensor2metric, I do preprocessing using these step
BET DTI image → denoise → eddy current correction → bias correction
After I run tensor2metric <input_image> -fa <output_image>
and the output image looks different from what we know…
Is that a command line error what I type? or just the image scale problem?
If the background is what is troubling you, you may add -mask mask_image of your whole brain while calculating fa from the tensor. tensor2metric — MRtrix 3.0 documentation
See The value of FA.nii.gz - #3 by jdtournier for an explanation of FA values larger than 1.
That does look odd for an FA map… May I ask whether these were acquired on a Phillips system? If so, this could be related to this issue – which I note we are not always able to detect correctly. If you can post the full output of
mrinfo <input image> -dwgrad, we might be able to spot the issue if that’s what it is…
The above pipeline does not list the dwi2tensor command.
Could it be that you are u are applying tensor2metric directly on the DWI data?