# 3dDWItoDT¶

```
Usage: 3dDWItoDT [options] gradient-file dataset
Computes 6 principle direction tensors from multiple gradient vectors
and corresponding DTI image volumes.
The program takes two parameters as input :
a 1D file of the gradient vectors with lines of ASCII floats:
Gxi, Gyi, Gzi.
Only the non-zero gradient vectors are included in this file (no G0
line).
** Now, a '1D' file of b-matrix elements can alternatively be input,
and *all* the gradient values are included!**
A 3D bucket dataset with Np+1 sub-briks where the first sub-brik is the
volume acquired with no diffusion weighting.
OUTPUTS:
+ you can output all 6 of the independent tensor values (Dxx, Dyy,
etc.), as well as all three eigenvalues (L1, L2, L3) and
eigenvectors (V1, V2, V3), and useful DTI parameters FA, MD and
RD.
+ 'Debugging bricks' can also be output, see below.
Options:
-prefix pname = Use 'pname' for the output dataset prefix name.
[default='DT']
-automask = mask dataset so that the tensors are computed only for
high-intensity (presumably brain) voxels. The intensity
level is determined the same way that 3dClipLevel works.
-mask dset = use dset as mask to include/exclude voxels
-bmatrix_NZ FF = switch to note that the input dataset is b-matrix,
not gradient directions, and there is *no* row of zeros
at the top of the file, similar to the format for the grad
input: N-1 rows in this file for N vols in matched data set.
There must be 6 columns of data, representing either elements
of G_{ij} = g_i*g_j (i.e., dyad of gradients, without b-value
included) or of the DW scaled version, B_{ij} = b*g_i*g_j.
The order of components is: G_xx G_yy G_zz G_xy G_xz G_yz.
-bmatrix_Z FF = similar to '-bmatrix_NZ' above, but assumes that first
row of the file is all zeros (or whatever the b-value for
the reference volume was!), i.e. there are N rows to the
text file and N volumes in the matched data set.
-bmatrix_FULL FF = exact same as '-bmatrix_Z FF' above (i.e. there are N
rows to the text file and N volumes in the matched data set)
with just a lot more commonsensical name. Definitely would
be preferred way to go, for ease of usage!
-scale_out_1000 = increase output parameters that have physical units
(DT, MD, RD, L1, L2 and L3) by multiplying them by 1000. This
might be convenient, as the input bmatrix/gradient values
can have their physical magnitudes of ~1000 s/mm^2, for
which typical adult WM has diffusion values of MD~0.0007
(in physical units of mm^2/s), and people might not like so
many decimal points output; using this option rescales the
input b-values and would lead to having a typical MD~0.7
(now in units of x10^{-3} mm^2/s). If you are not using
bmatrix/gradient values that have their physical scalings,
then using this switch probably wouldn't make much sense.
FA, V1, V2 and V3 are unchanged.
-bmax_ref THR = if the 'reference' bvalue is actually >0, you can flag
that here. Otherwise, it is assumed to be zero.
At present, this is probably only useful/meaningful if
using the '-bmatrix_Z ...' or '-bmatrix_FULL ...'
option, where the reference bvalue must be found and
identified from the input info alone.
-nonlinear = compute iterative solution to avoid negative eigenvalues.
This is the default method.
-linear = compute simple linear solution.
-reweight = recompute weight factors at end of iterations and restart
-max_iter n = maximum number of iterations for convergence (Default=10).
Values can range from -1 to any positive integer less than
101. A value of -1 is equivalent to the linear solution.
A value of 0 results in only the initial estimate of the
diffusion tensor solution adjusted to avoid negative
eigenvalues.
-max_iter_rw n = max number of iterations after reweighting (Default=5)
values can range from 1 to any positive integer less
than 101.
-eigs = compute eigenvalues, eigenvectors, fractional anisotropy and mean
diffusivity in sub-briks 6-19. Computed as in 3dDTeig
-debug_briks = add sub-briks with Ed (error functional), Ed0 (orig.
error), number of steps to convergence and I0 (modeled B0
volume).
[May, 2017] This also now calculates two goodness-of-fit
measures and outputs a new PREFIX_CHI* dset that has two
briks:
brik [0]: chi^2_p,
brik [1]: chi^2_c.
These values are essentially calculated according to
Papadakis et al. (2003, JMRI), Eqs. 4 and 3,
respectively (in chi^2_c, the sigma value is the
variance of measured DWIs *per voxel*). Note for both
chi* values, only DWI signal values are used in the
calculation (i.e., where b>THR; by default,
THR=0.01, which can be changed using '-bmax_ref ...').
In general, chi^2_p values seem to be <<1, consistent
with Papadakis et al.'s Fig. 4; the chi^2_c values are
are also pretty consistent with the same fig and seem to
be best viewed with the upper limit being roughly =Ndwi
or =Ndwi-7 (with the latter being the given degrees
of freedom value by Papadakis et al.)
-cumulative_wts = show overall weight factors for each gradient level
May be useful as a quality control
-verbose nnnnn = print convergence steps every nnnnn voxels that survive
to convergence loops (can be quite lengthy).
-drive_afni nnnnn = show convergence graphs every nnnnn voxels that
survive to convergence loops. AFNI must have NIML
communications on (afni -niml)
-sep_dsets = save tensor, eigenvalues, vectors, FA, MD in separate
datasets
-csf_val n.nnn = assign diffusivity value to DWI data where the mean
values for b=0 volumes is less than the mean of the
remaining volumes at each voxel. The default value is
'1.0 divided by the max bvalue in the grads/bmatrices'.
The assumption is that there are flow artifacts in CSF
and blood vessels that give rise to lower b=0 voxels.
NB: MD, RD L1, L2, L3, Dxx, Dyy, etc. values are all
scaled in the same way.
-min_bad_md N = change the min MD value used as a 'badness check' for
tensor fits that have veeery (-> unreasonably) large MD
values. Voxels where MD > N*(csf_val) will be treated
like CSF and turned into spheres with radius csf_val
(default N=100).
-csf_fa n.nnn = assign a specific FA value to those voxels described
above The default is 0.012345678 for use in tractography
programs that may make special use of these voxels
-opt mname = if mname is 'powell', use Powell's 2004 method for
optimization. If mname is 'gradient' use gradient descent
method. If mname is 'hybrid', use combination of methods.
MJD Powell, "The NEWUOA software for unconstrained
optimization without derivatives", Technical report DAMTP
2004/NA08, Cambridge University Numerical Analysis Group:
See: http://www.ii.uib.no/~lennart/drgrad/Powell2004.pdf
-mean_b0 = use mean of all b=0 volumes for linear computation and initial
linear for nonlinear method
Example:
3dDWItoDT -prefix rw01 -automask -reweight -max_iter 10 \
-max_iter_rw 10 tensor25.1D grad02+orig.
The output is a 6 sub-brick bucket dataset containing
Dxx, Dxy, Dyy, Dxz, Dyz, Dzz
(the lower triangular, row-wise elements of the tensor in symmetric matrix
form). Additional sub-briks may be appended with the -eigs and -debug_briks
options. These results are appropriate as the input to 3dDTeig.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100..200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
```