7.1.72. 3dEigsToDTΒΆ

Link to classic view

Convert set of DTI eigenvectors and eigenvalues to a diffusion tensor, while also allowing for some potentially useful value-scaling and vector- flipping.

May be helpful in converting output from different software packages. Part of FATCAT (Taylor & Saad, 2013) in AFNI. It is essentially the inverse of the existing AFNI command: 3dDTeig.

Minor note and caveat: This program has been checked for consistency with 3dDWItoDT outputs (that is using its output eigenvalues and eigenvectors to estimate a DT, which was then compared with that of the original 3dDWItoDT fit). This program will mostly return the same DTs that one would get from using the eigenvalues and eigenvectors of 3dDWItoDT to very high agreement The values generally match to <10**-5 or so, except in CSF where there can be small/medium differences, apparently due to the noisiness or non- tensor-fittability of the original DWI data in those voxels. However, these discrepancies shouldn’t really affect most cases of using DTI data. This is probably generally true for reconstructing DTs of most software program output: the results match well for most WM and GM, but there might be trouble in partial-volumed and CSF regions, where the DT model likely did not fit well anyways. Caveat emptor.

  • COMMAND: 3dEigsToDT -eig_vals NAME1 -eig_vecs NAME2 {-mask MASK }
{-flip_x | -flip_y | flip_z} {-scale_eigs X} -prefix PREFIX
    • OUTPUT:
      1. AFNI-format DT file with 6 subbricks in the same format as output

        by, for example, 3dDWItoDT (the lower triangular, row-wise elements of the tensor in symmetric matrix form)

        [0] Dxx [1] Dxy [2] Dyy [3] Dxz [4] Dyz [5] Dzz

    • RUNNING: -eig_vals NAME1 :Should be a searchable descriptor for finding all

      three required eigenvalue files. Thus, on a Linux commandline, one would expect: $ ls NAME1 to list all three eigenvalue files in descending order of magnitude. This program will also only take the first three matches (not including doubling of BRIK/HEAD files in AFNI-format).

      -eig_vecs NAME2 :Should be a searchable descriptor for finding all

      three required eigenvector files. Thus, on a Linux commandline, one would expect: $ ls NAME2 to list all three eigenvector files in order matching the eigenvalue files. This program will also only take the first three matches (not including doubling of BRIK/HEAD files in AFNI-format).

      -> Try to make NAME1 and NAME2 as specific as possible, so

      that the search&load gets everything as right as possible. Also, if using the wildcard character, ‘*’, then make sure to enclose the option value with apostrophes (see EXAMPLE, below).

      -prefix PREFIX :output file name prefix. Would suggest putting a ‘DT’

      label in it.

      -mask

      MASK :can include a mask within which to calculate uncert. Otherwise, data should be masked already.

      -flip_x

      :change sign of first element of eigenvectors.

      -flip_y

      :change sign of second element of eigenvectors.

-flip_z :change sign of third element of eigenvectors.
-> Only a single flip would ever be necessary; the combination
of any two flips is mathematically equivalent to the sole application of the remaining one.
-scale_eigs X :rescale the eigenvalues, dividing by a number that is X>0. Could be used to reintroduce the DW scale of the original b-values, if some other program has remorselessly scaled it away.
    • ** * ** * ** * ** * ** * ** * ** * ** * ** * ** * ** * ** * ** * ** * **
    • EXAMPLE:

      3dEigsToDT -eig_vals ‘DTI/DT_L*’ -eig_vecs ‘DTI/DT_V*’ -prefix DTI/NEW_DT -scale_eigs 1000 -flip_y

    If you use this program, please reference the introductory/description

    paper for the FATCAT toolbox: Taylor PA, Saad ZS (2013). FATCAT: (An Efficient) Functional And Tractographic Connectivity Analysis Toolbox. Brain Connectivity.

Table Of Contents

This Page