Difference between revisions of "CTPhantomSegmentation"

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We scanned a phantom (plastic skull) in a water bag with contrast agent mixed into water. This gives the outline of the skull as dark, whereas the water enhances. In order to be used in the navigation system, need to make background dark (~0), and plastic area light in an intensity range similar to tissue.
 
  
Here are the steps used to create:
 
 
1) segment the phantom dicom series number 8 (T2 sequence) using Seg3D.
 
First used threshold selection to get the outline; then manually
 
deleted spots at which there was a bridge between (~0 intensity) skull
 
voxels and exterior voxels (in frame but outside plastic/water; also 0); also cleaned up extraneous things
 
where were obviously not skull; then ran a connected component filter to
 
grab only the connected skull voxels. Then did "Export Segmentation",
 
and re-loaded as Volume (binary mask at this point). Applied Gaussian
 
Distortion filter to image.
 
 
2) From Seg3D, saved image as nrrd, then loaded in Slicer. Used the
 
Converters->Reorient Images module to change orientation to RPI (because
 
Analyze only supports this and 2 other orientations; when I first tried
 
writing Analyze, the orientation came out wrong).
 
 
3) Saved image as Analyze pair from Slicer (hdr/img). Reloaded to check
 
that orientation was correct.
 
 
4a) Loaded resulting image in matlab using spm commands. The output from
 
step (1) is in range [0,1] so multiplied by 3000 to get values which
 
roughly correspond to what we would get for a patient scan (0.9 -> 2700
 
which is a little high but ok).
 
 
4b) Ran resulting image through matlab script which takes Analyze data
 
and makes a DICOM series by concatenating each slice data onto the
 
original DICOM headers (from which the Analyze was originally created).
 
 
5) Loaded script output series in Seg3D to check against original (the
 
Slicer dicom reader is broken and would not read these DICOMs correctly.
 
Seg3D and BL read fine).
 
 
Then I took data to BrainLab planning station on USB stick and loaded
 
using patXfer to create a patient plan for "phantom". The model images
 
linked above were generated by BL iPlan without intervention.
 
 
[[Image:inorton_Phantom_SS1.png]]
 
 
[[Image:inorton_Phantom_SS2.png]]
 
 
[[Image:inorton_Phantom_SS3.png]]
 
 
[[Image:inorton_Phantom_SS4.png]]
 

Latest revision as of 16:12, 13 July 2018

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