Andy: /* Estimating and visualizing tensors */

2006-12-20T15:55:54Z

Estimating and visualizing tensors

Andy: Update from Wiki

2006-12-18T13:37:41Z

Update from Wiki

New page

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:

<div class="thumb tright"><div style="width: 182px">[[Image:000000.png|[[Image:180px-000000.png|Glyphs for synthetic helical DWI dataset]]]]<div class="thumbcaption"><div class="magnify" style="float: right">[[Image:000000.png|[[Image:magnify-clip.png|Enlarge]]]]</div>Glyphs for synthetic helical DWI dataset</div></div></div>

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.

@@ Line 124: / Line 124: @@
 Because the camera and glyph parameters are set on the command-line, the following image should come up:
-<div class="thumb tright"><div style="width: 182px">[[Image:000000.png|[[Image:180px-000000.png|Glyphs for synthetic helical DWI dataset]]]]<div class="thumbcaption"><div class="magnify" style="float: right">[[Image:000000.png|[[Image:magnify-clip.png|Enlarge]]]]</div>Glyphs for synthetic helical DWI dataset</div></div></div>
+[[Image:000000.png|thumb|right|180px|Glyphs for synthetic helical DWI dataset]]
 The following things should be noted:

NAMIC Wiki:DTI:HelixDWI - Revision history

Andy: /* Estimating and visualizing tensors */

Andy: Update from Wiki