FD/FC/FDC for a single tract


#1

Dear expert,
I am performing fixel based analysis. My questions are

  1. How can I read the value of FD or FC or FDC from a single voxel for an individual subject? I do not want to perform group analysis.
  2. For a streamline how can I calculate FD FC FDC for each of the fibre bundles ?

I have extract total number of streamlines between two ROIs.
I have performed track to fixel.
I have performed fixel to tsf and saw the track scaler file in mrview, but how I can not calculate the FD for a fibre bundle i.e track.
Please let me know if I can do so.
Many thanks!
Sarbani


#2

Hi Sarbani,

It sounds like you’re trying to do something similar to other recent posts; e.g. see here. But I’ll try to address these in turn as best I can:

How can I read the value of FD or FC or FDC from a single voxel for an individual subject?

voxel2fixel using a ROI containing a single voxel will generate a fixel mask selecting only those fixels within that one voxel. You could then access the raw metric values using mrdump -mask.

You could even generate the single-voxel ROI at the command-line using the mredit command if you so desired.

For a streamline how can I calculate FD FC FDC for each of the fibre bundles ?

One would not normally describe a solitary streamline having an association with a plurality of “fibre bundles”… Do you perhaps mean that you want the FD / FC / FDC values for all fixels traversed by an individual streamline? Unfortunately while tcksample is the logical place to look for such a functionality, it does not yet have the capacity to work with fixels (that’s one small part of a large software update I’ve been working on for ages, and may finish before the end of the universe if I’m lucky). You could however pull a bit of a trick by using the tck2fixel command, followed by mrthreshold -abs 0.5, to get a fixel mask containing only those fixels traversed by that particular streamline. You would however lose in this process the information regarding the order in which those fixels were traversed.

Rob