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Brian Wandell edited this page Jul 22, 2016 · 22 revisions
          ______________ <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

The following table provides some information about the different background images produced by dtiInit.

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:dti_fa.jpg ||

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.)'']

|'''vRGB''' || Image:dti_vrgb.jpg ||

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''' || Image:dti_t1.jpg || 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'' [http://www.sinauer.com/detail.php?id=2887 ''(Ref.)''] |}

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