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DWI Files

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Brian Wandell edited this page Oct 23, 2016 · 22 revisions

Overview

The following files are produced by the dtiInit analysis. Below is information about the different files and images.

          ______________ <subdir> ____________
    _____|_____                               |
   |           |                              |   
t1.nii.gz      raw                        <Directory: dtiNumDirsInterpMethod>      
               |                  ____________|_____________
            dwi.nii.gz           |            |             |
            dwi.bval            bin        dt6.mat      t1pdd.png
            dwi.bvec             |
                           tensors.nii.gz
                           b0.nii.gz
                           brainMask.nii.gz
                           vectorRGB.nii.gz
                           wmMask.nii.gz
                           wmProb.nii.gz
                           faStd.nii.gz
                           mdStd.nii.gz
                           pddDispersion.nii.gz

On the left, the t1.nii.gz and dwi files are the inputs. The other files are produced by dtiInit.

To check: Are the images all in the T1-aligned coordinate frame?

  • dt6.mat - Contains ...
  • tensors.nii.gz - Estimated diffusion tensors (different methods for computing, why we compute them)
  • b0.nii.gz - The mean b=0 data that are used for alignment to the T1 anatomical (I think; but does this mean they are not aligned to the T1? Or is this after the raw B=0 are aligned?)
  • brainMask.nii.gz - In the aligned frame
  • wmMask - White matter mask
  • vectorRGB - Principal diffusion direction data as a color map
  • wmProb.nii.gz -
  • faStd - Fractional anisotropy calculation
  • mdStd - Mean diffusivity
  • pddDispersion -

Background images

B0 Image

The b0 image is the non-diffusion-weighted image. It is an image acquired with a b-value (diffusion weighting strength) of 0.

MD

Mean diffusivity (MD) is the mean of the eigenvalues of the diffusion tensor or, equivalently, the trace of the diffusion tensor divided by 3. This parameter quantifies the size of the diffusion ellipsoid. The MD measure is invariant with respect to the orientation of the diffusion tensor and tends to vary little across brain tissue.

FA Image

Fractional anisotropy (FA) is a measure of the degree of anisotropy in a tensor model of diffusion at a given voxel. FA values are bounded between zero (a perfect shape) and one (an infinitely long cigar shape).
''In the FA map FA values closer to one appear brighter.'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17379499&dopt=Abstract ''(Ref.)'']

PDD RGB

The Vector RGB color map is created from FA values and the three vector elements. The three colors in this map correspond to the direction of the largest eigenvalue of the diffusion tensor (principle diffusion direction) with proportional intensity according to the FA.
''RED = left/right, BLUE = superior/inferior, and GREEN = anterior/posterior.'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17379499&dopt=Abstract ''(Ref.)'']

T1 weighted image

The T1 weighted image provides structural contrast for anatomical images of the brain. The relative signal intensity of voxels within the image depends upon the T1 value of the tissue in that voxel.
''Tissues that have a smaller T1 value appear brighter than those with larger values:''
''(White matter T1 value = ~600ms. Gray matter T1 value = ~900ms. Cerebrospinal fluid T1 value = ~4000ms) - all values for Field strength of 1.5T''

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