DTI Quality Control - Part 2: Tensor fitting

Thursday, March 06, 2014 Do Tromp 0 Comments



After making sure your data was acquired correctly (see also this post) and all looked good - you can go ahead and start tensor fitting. At the core of tensor fitting is using the right gradient directions and sometimes (for programs like Camino) creating a so called "scheme file". A scheme file consists of both the b-values and b-vectors. The b-values are the amount of diffusion weighting used for each volume. Depending on how many non-diffusion weighted or B0 scans you collect (read more on its use here) and what diffusion weighting max you use your b-value file is going to look something like this (shortened version):
0,0,0,0,0,0,1000,1000,1000,1000,1000,1000,1000,1000,1000,1000,1000

Your b-vector are the gradient directions that you collect, often predetermined by the scanner depending on how many total directions you choose to collect. A b-vector file will look something like this (shortened version):
b-vectors

 The b-vectors consist out of 3 separate vectors (x, y, z) for each direction acquired. A program like fsl2scheme (more info here) will be able to combine the b-values and b-vectors into a scheme file. Together looking something like this (note that there are 4 b0 slices visible, while the scheme file only shows 1 b0):

Scheme file, next to diffusion volumes

 If you run a eddy correction it is advisable to correct your scheme file for the induced movement of each volume after registration. Here are a couple of resources to help you with this: 
http://blog.cogneurostats.com/?p=302
http://onlinelibrary.wiley.com/doi/10.1002/mrm.21890/abstract
https://github.com/bernardng/codeSync/blob/master/dMRIanalysis/rotatebvecs
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;3c23f260.0903
After running the tensor fitting command you will have to check if the vectors were applied correctly. In the below examples we are using Camino's pdview, but you can use any program that allows you to view the tensors. You should check the axial, coronal and sagittal views. As a reference the corpus callosum can be used, the tensors should follow the shape of the corpus callosum (in red) in a fluid motion, as in the examples below:

Axial view
Coronal view
Sagittal view

EXAMPLES OF WRONG ORIENTATION:

Notice the tensor orientations in corpus callosum (red area)
Wrong orientation

Fix it by adjusting the scheme file:

There are multiple options to correct the scheme file in the fsl2scheme command:
- add -usegradmod(usually when error pops up)
- add -flipx
- add -flipy
- add -flipz
- or any combination of the above, eg. as used in the example above: fsl2scheme -bvecfile bvecs.txt -bvalfile bvals.txt -flipx -flipy -usegradmod prefix.scheme


EXAMPLE OF WRONG COLOR:

Notice the blue corpus callosum
Wrong orientation

Fix it by adjusting the b-vector table:

- In the bvecs text file, swap the x and z row with the directions.
- And in this specific case: fsl2scheme -bvecfile bvecs_zx.txt -bvalfile bvals.txt -flipx -flipz -usegradmod prefix.scheme


ANOTHER EXAMPLE:

Notice the green corpus callosum
Wrong orientation

Fix it by adjusting the b-vector table:

- In the bvecs text file, swap the x and y row.
- And in this specific case: fsl2scheme -bvecfile bvecs_yx.txt -bvalfile bvals.txt -usegradmod prefix.scheme

Remember:
x - Red
y - Green
z - Blue