Group TDIs and/or VBA


#1

Hi all,

I want to generate an average TDI image for subjects in two groups (from single shell data) and compare them either qualitatively or, better, quantitatively (as in a voxel-based analysis as suggested is possible in Calamente et al. 2010)

For qualitative comparison, I was thinking to simply:

1- perform preprocessing: denoising and unringing; motion and distortion correction; bias field correction; and global intensity normalisation across subjects
2- estimate response function; perform CSD; perform tractography (ACT); perform SIFT1
3- to normalise the tracts, use tcktransform (as detailed in this post), after generating (e.g., in SPM), and correcting (with warpcorrect) the necessary warps.
4- perform tckmap on the resulting normalised tracts (as specified in this post).
5- Average across participants within group and compare output

Couple of questions: if using tcksift2, is there a way to normalise the weights or apply them to images in standard space? Similarly, could/should mu (from sift1 in step 2 above) be applied to normalised TDIs?

For quantitative comparison, I think perhaps a modified version of the single shell FBA pipeline could work:

  1. perform preprocessing: denoising and unringing; motion and distortion correction; bias field
    correction; and global intensity normalisation across subjects
  2. compute an (average) white matter response function
  3. upsample DW images
  4. compute upsampled brain mask images
  5. Fibre Orientation Distribution estimation (spherical deconvolution)
  6. generate a study-specific unbiased FOD template
  7. register all subject FOD images to the FOD template
  8. compute the template mask (intersection of all subject masks in template space)
  9. warp FOD images to template space (with reorientation)
  10. perform whole-brain fibre tractography on all subject FOD images in template space
    using template mask as seed
  11. perform SIFT2 on subject tractograms in template space
  12. generate tract density images (TDI) for each subject (and multiply by the respective mu value?)
  13. average TDIs across individuals per group; perform VBA

Your thoughts on the above two approaches is very much appreciated.

Juan


#2

Hi Juan,

The wording of the possibility of performing VBA on TDI data within the 2010 manuscript has been a cause of regret for all involved.

I would strongly advise reading this manuscript to see why your proposed experiment is in fact an inferior alternative to what we already have with FBA.

Rob