Mean FA of fibres crossing a ROI

My apology to bring up this old topic again.

I am a medical student trying to work on DWI data on some patient data.

I have been trying to do something very very similar to Marlene, to obtain mean FA of any fire crossing my ROI.

I would like to create the fixel mask from my ROI mask (voxel) starting with the function voxel2fixel. However, it was not too intuitive for beginner like me to see how may I proceed.

If I may clarify on how to use the function voxel2fixel here:

voxel2fixel [ options ] image_in fixel_directory_in fixel_directory_out fixel_data_out

May I know what should be my fixel_directory_in? In addition, may I know what would be the output difference between fixel_directory_out and fixel_data_out?

Again, thank you for clarifying this.

Best regards

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Hi @arthuryong,

I’ve moved your post to a new topic since I think what you are trying to achieve here differs from that from the original topic where it was posted.

I want to focus specifically on this part:

mean FA of any fibre crossing my ROI

If this is indeed an accurate description of what you are trying to do, then there is no need to engage with the fixel directory format or any commands that operate on such: FA is a scalar voxel-wise measure, and streamlines data are entirely different in nature to fixel data.

If I take this description literally, then what you want to do (in this order) is:

  1. Extract the subset of streamlines that traverse your ROI (tckedit -include)

  2. Obtain the mean FA along each of those streamlines (tcksample -stat_tck mean)

Let me know if this is not an accurate understanding of what you’re trying to do