[Insight-developers] NRRD Image Format

[Vincent A. Magnotta]

I am trying to use the NRRD format to store diffusion weighted images. I
have been using the information provided on the NA-MIC website:

http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki%3ADTI%3ATensor_format

It appears that the ITK implementation for diffusion weighted images
does not work properly. From just a first pass analysis, it seems that
if the NRRD file describes an image that is 4D, but it only has three
spatial dimensions, the 4th dimension upon loading the images has a size
of only 1. I have a very small image example that illustrates the
problem that is attached. When I print out the image after loading it, I
get the following information:


Image (0x84e5bd8)
  RTTI typeinfo:   itk::Image<short, 4>
  Reference Count: 2
  Modified Time: 131
  Debug: Off
  Observers:
    none
  Source: (none)
  Source output index:  0
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 11
  UpdateMTime: 130
  LargestPossibleRegion:
    Dimension: 4
    Index: [0, 0, 0, 0]
    Size: [2, 2, 2, 1]
  BufferedRegion:
    Dimension: 4
    Index: [0, 0, 0, 0]
    Size: [2, 2, 2, 1]
  RequestedRegion:
    Dimension: 4
    Index: [0, 0, 0, 0]
    Size: [2, 2, 2, 1]
  Spacing: [2, 2.5, 2, 1]
  Origin: [0, 0, 0, 0]
  Direction:
-1 0 0 0
0 -1 0 0
0 0 1 0
0 0 0 1

I will look into this some more over the next couple of days, but I
thought that I would post it here as well. I am just getting familiar
with the format, so if anyone else has suggestions they would be
helpful.

Vince



-- 
Assistant Professor
Department of Radiology
0453-D JCP
200 Hawkins Drive
Iowa City, IA 52242
E-mail: vincent-magnotta at uiowa.edu
Phone: 319-356-8255
Fax: 319-353-6275
Website: http://www.radiology.uiowa.edu
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NRRD0005
content: SomeIDNumber42
type: short
dimension: 4
space: right-anterior-superior
sizes: 2 2 2 2
thicknesses:  NaN  NaN 2.5  NaN
space directions: (2,0,0) (0,2.5,0) (0,0,2) none
centerings: cell cell cell none
kinds: space space space list
endian: little
encoding: ascii
space units: "mm" "mm" "mm"
space origin: (0,0,0)
data file: tmp.img
measurement frame: (1,0,0) (0,0,1) (0,1,0)
modality:=DWMRI
DWMRI_b-value:=1000
DWMRI_gradient_0000:= 0  0  0
DWMRI_gradient_0001:= 1  0  1