DWI Files

Overview

The following folders and files are produced by the dtiInit analysis. Information about the different files and images.

          ______________ <subdir> ____________
    _____|______________                      |
   |           |        |           <dtiNumDirsInterpMethod> 
t1.nii.gz      raw    ROIS                    |
               |                  _________|________________________________________
            dwi.nii.gz           |         |          |           |               |
            dwi.bval            bin     dt6.mat   t1pdd.png    dtiInit-log.mat   fibers
            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

The input files are n the left: the t1.nii.gz and the dwi files. The output files dtiInit are in the folders on the right. The name of this folder reflects

• numDirs - the number of diffusion directions measured
• InterpMethod - the interpolation method

Examples are dti31trilin or dti60trilinrt (robust tensor fitting). In a typical analysis, we might align the DWI data to the b=0 measurements using a trilinear interpolation method with eddy current correction turned on.

Top level output files

• dt6.mat - This is the main file fed in to the mrDiffusion UI that is part of vistasoft.
• dtiInit-log.mat - The parameters submitted to dtiInit are stored here. There are also technical specifications for reproducibility (various shah codes, versions, and so forth).
• t1pdd.png - A T1 background (either yours or the MNI template if you didn't have one) and the principal diffusion directions as an RGB overlay

The fibers directory is where we store, um, fibers. The bin directory is where we store various derived quantities that are used for computation.

The bin directory output files

All of the files in this directory are in the 'aligned' and 'interpolated' coordinate frame. Usually they are also cropped to include only the region around the brain. The cropping saves a little space but changes the from the original data.

• tensors.nii.gz - Estimated diffusion tensors (different methods for computing, why we compute them)
• b0.nii.gz - The mean of the b=0 measurements. These data are resampled and interpolated the same way the data are interpolated. 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 - Binary mask of the brain locations
• wmMask - Binary mask of the white matter locations
• vectorRGB - Principal diffusion direction data as a color map
• wmProb.nii.gz - Not sure, but its range is 0,255 for some reason
• faStd - Fractional anisotropy values at each brain location
• mdStd - Mean diffusivity values at each brain location
• pddDispersion -

Background images

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

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.

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.)'']

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.)'']

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''