Extract FD value in ROI

Hello MRtrix3 Team,

I have followed steps of FBA analysis,but I want to extract FD value in ROI for each subject,not the whole brain.
How can I do?

Thanks for you help.

Hi Wang,

The tricky part of this question is the derivation of an appropriate mask within which you wish to extract the values of FD. Once you have that issue sorted, you have a fixel data file containing FD values, and a fixel data file containing a binary mask (1 for fixels to include, 0 for fixels to not include); these can then be used in a similar way to 3D images, e.g. mrstats with the -mask option to compute summary statistics within the mask, or to mrdump -mask to obtain the exhaustive list of FD values within the mask.

Producing such a fixel mask (as opposed to just a 3D voxel mask) can however require some manipulation. Ideally I’d like to have the mrview ROI tool capable of manually editing fixel masks, but I’ve not even so much as started writing that code. So you’re stuck with the commands / capabilities that are available currently. Some useful ideas:

  • Generating / selecting a set of streamlines corresponding to a pathway of interest (tckgen / tckedit), then generating from this a fixel data file containing the number of intersecting streamlines per fixel (tck2fixel), then thresholding this (mrthreshold);

  • Projecting a 3D voxel ROI up to the fixels within each voxel (voxel2fixel);

  • Selecting only fixels above a certain fibre density in template space (mrthreshold);

  • Calculating intersections between masks derived from different information sources (mrcalc -mult).

I’m sure others here have played around in this space and may have suggestions.


Thank you very much!