Fibre orientation wrt B0

[lottevdvoort]

Hi @ThijsDhollander,
Thanks for your elaboration on the matter!

@ThijsDhollander

Depending on what you want to do with the result, maybe a fixel image is not what you want to deal with…?

The goal is to compare R2* values to the fibre orientation and see how those relate, so I reckon a voxel image would be necessary in order to do so.

@ThijsDhollander

A mean direction of the entire FOD “as whole” of course makes less sense if there’s multiple fibre orientations

You’re right, I was a bit sloppy with my words.

A couple of other questions:

• If I want to calculate the angle of the second largest fixel wrt B0, I change the number in the first line to 2 and the coordinates to 3 5, right?
• Is there a way to visualise only the second largest fixels? Looking at the peak_direction.mif when using -number 2 gives both the largest and second largest fixels. Is there any way to extract only the second largest one from that file? Not really an important thing but would be nice for visualising the process.
• What exactly is meant by the ‘largest’ fixel; is this based on the afd?

Thanks for your help!