View source for NAMIC Wiki:DTI:HelixDWI

This page shows how to use Teem command-line tools to create a synthetic DWI dataset in NRRD format, which can be used to verify a given piece of software's handling of the coordinate frames involved, especially the measurement frame.

Running these commands requires a version of Teem more recent than version 1.9.0, the version shipping with Slicer 2.6. However, the datasets can be downloaded from here without regenerating them.

=== Creating the gradient list ===

 
 tend grads -n 12 \
  | unu pad -min 0 -1 -max M M -b pad -v 0 -o grads.txt

This generates a set of gradient directions, pre-pended with a zero vector (for a baseline image). The result should be the text file "<tt>grads.txt</tt>" with contents:

 
 0 0 0
 0.045864213 -0.97327703 -0.22500728
 0.25820592 -0.47978204 0.83853376
 -0.40941855 -0.2207699 0.88523281
 0.90057635 -0.041144647 -0.43274629
 0.9589954 -0.024969423 0.28231958
 -0.53121203 -0.12678577 -0.8376987
 -0.75857437 -0.61072785 0.22710435
 -0.65501362 0.7005415 -0.28319383
 0.56272566 0.69972253 0.44014561
 0.10537088 -0.45475256 -0.88436252
 -0.62760335 0.64766514 0.43202299
 0.15000534 0.88426256 -0.44224218

=== Creating the synthetic tensor field ===

 
 tend helix -s 29 30 31 -ip 0.1 0.3 0.6 -mp -0.8 0.1 0.4 -r 40 -o ten.nrrd

This program generates a tensor field where the anisotropy tensors are along a right-handed helix, with the tensors themselves displaying a particular kind of twist.

To make things interesting, the image orientation and measurement frames are set to something non-axis-aligned, via the "<tt>-ip 0.1 0.3 0.6</tt>" and "<tt>-mp -0.8 0.1 0.4</tt>" options respectively, and these determine the "<tt>space directions</tt>" and "<tt>measurement frame</tt>" fields. They can be inspected via:

 
 unu head ten.nrrd

 <nowiki>
 NRRD0005
 # Complete NRRD file format specification at:
 # http://teem.sourceforge.net/nrrd/format.html
 type: float
 dimension: 4
 space: right-anterior-superior
 sizes: 7 29 30 31
 space directions: none (2.645253,5.951819,-2.267359) (-5.205479,3.287671,2.557078) (3.181617,0.707026,5.56783)
 centerings: ??? cell cell cell
 kinds: 3D-masked-symmetric-matrix space space space
 endian: big
 encoding: raw
 space origin: (-9.278346,-141.602085,-88.852048)
 measurement frame: (0.812155,0.353591,-0.464088) (-0.530387,0.116022,-0.839779) (-0.243094,0.928177,0.281768)
 </nowiki>

=== Creating the synthetic DWI data (.nhdr and .raw available) ===

First we have to invent a baseline T2 image:

 
 tend helix -s 29 30 31 -ip 0.1 0.3 0.6 -mp -0.8 0.1 0.4 -r 50 \
  | tend anvol -a fa \
  | unu 2op x - 7000 -o b0.nrrd

This is a little silly- its just making a new tensor volume with a fatter radius ("-r 50" instead of "-r 40"), then measuring fractional anisotropy everywhere, multiplying it by 7000, then saving it out to a scalar nrrd volume.

Then, the DWI value simulation is done based on the baseline image and synthetic tensors:

 
 tend sim -g grads.txt -r b0.nrrd -i ten.nrrd \
   -b 800 -t ushort -kvp -o dwi-D.nhdr

This results in a NRRD DWI header of the same form that is created for measured DWI scans:

* [[Image:Dwi-D.nhdr|Image:Dwi-D.nhdr]]<nowiki>: the detached NRRD header </nowiki>
* [[Image:Dwi-D.raw|Image:Dwi-D.raw]]<nowiki>: the single raw file (same directory as .nhdr file) </nowiki>

 <nowiki>
 NRRD0005
 # Complete NRRD file format specification at:
 # http://teem.sourceforge.net/nrrd/format.html
 content: (unsigned short)(???)
 type: unsigned short
 dimension: 4
 space: right-anterior-superior
 sizes: 13 29 30 31
 space directions: none (2.645253,5.951819,-2.267359) (-5.205479,3.287671,2.557078) (3.181617,0.707026,5.56783)
 centerings: ??? cell cell cell
 kinds: list space space space
 endian: big
 encoding: raw
 space origin: (-9.278346,-141.602085,-88.852048)
 measurement frame: (0.812155,0.353591,-0.464088) (-0.530387,0.116022,-0.839779) (-0.243094,0.928177,0.281768)
 data file: dwi-D.raw
 modality:=DWMRI
 DWMRI_b-value:=800
 DWMRI_gradient_0000:=0 0 0
 DWMRI_gradient_0001:=0.0458642 -0.973277 -0.225007
 DWMRI_gradient_0002:=0.258206 -0.479782 0.838534
 DWMRI_gradient_0003:=-0.409419 -0.22077 0.885233
 DWMRI_gradient_0004:=0.900576 -0.0411446 -0.432746
 DWMRI_gradient_0005:=0.958995 -0.0249694 0.28232
 DWMRI_gradient_0006:=-0.531212 -0.126786 -0.837699
 DWMRI_gradient_0007:=-0.758574 -0.610728 0.227104
 DWMRI_gradient_0008:=-0.655014 0.700541 -0.283194
 DWMRI_gradient_0009:=0.562726 0.699723 0.440146
 DWMRI_gradient_0010:=0.105371 -0.454753 -0.884363
 DWMRI_gradient_0011:=-0.627603 0.647665 0.432023
 DWMRI_gradient_0012:=0.150005 0.884263 -0.442242
 </nowiki>

=== Estimating and visualizing tensors ===

This uses "<tt>tend estim</tt>" to estimate tensors with linear-least-squares on the log(DWI), and then passes them to the Deft program for visualization:

 
 tend estim -i dwi-D.nhdr -knownB0 false -B kvp -o - \
  | Deft_dti -i - -a fa -gsc 1200 -atr 0.65 \
   -fr 940.805 307.575 1025.14 -at 0 0 0 \
   -up -0.521774 -0.557152 0.646014 -rh -ar \
   -dn -164.709 -df 164.709 -fv 5.41056 -is 640 480

Because the camera and glyph parameters are set on the command-line, the following image should come up:

[[Image:000000.png|thumb|right|180px|Glyphs for synthetic helical DWI dataset]]

The following things should be noted:

* The region of anisotropy is helical. The spatial axis sizes were all unequal ("<tt>-s 29 30 31</tt>."), so if these are interpreted incorrectly (e.g. slow to fast instead of fast to slow), the anisotropic region will not appear as a simple helix.
* The helix is right-handed, like a DNA strand. As your right hand thumb moves along the axis of the helix, curling your fingers follows the path of the helix. If you see a left-handed helix, the handed-ness of your coordinate system is wrong.
* Along the surface of the helical path, the glyphs also rotate along a right-handed helix. If the tensors do not have this consistent surface-aligned appearance, there is something wrong with your handling of the measurement frame.