Difference between revisions of "Medical Imaging Example Meshes"

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__TOC__
 
__TOC__
−
=2D Example Meshes=
 
−
The directory containing the 2D input data is located in the 2D folder of [https://odu.box.com/s/wd0i18giti2zo330y19xhkqu8wjzgf7j Medical_Imaging_Data].
 
  
−
The image data were acquired from [https://www.cdc.gov/media/subtopic/images.htm Centers for Disease Control and Prevention]
+
=3D Example Meshes=
 +
The directory containing the 3D input data is located in the 3D folder of [https://odu.box.com/s/olefferrnksu2nmerbfvbvsz2u4abbdw Medical_Imaging_Data].
  
−
==COVID-19-23354==
+
==Ircad2==
−
* Input image : Dimensions (3,000x2,000) with spacing (1x1)
+
* [https://odu.box.com/s/1ef11ry4yik5mny62dz6zyd9obqb540i Input Image]
−
* Uniform with Min-Edge = 15: 82,981 triangles
+
* Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002)
−
* Adaptive with Min-Edge = 15: 67,920 triangles
+
* Uniform with Delta = 2: 5,031,442 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
 +
* Graded with Delta = 1: 6,072,751 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
 +
* Uniform with Delta = 2 and excluded label 1: 1,941,468 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
  
−
<gallery mode="packed" heights=250px>
+
<gallery mode="packed" heights=350px>
−
File:COVID-19-23354,uniform,e=15,suface.png
+
File:Ircad2,d=2.png
−
File:COVID-19-23354,uniform,e=15,triangulation.png
+
</gallery>
−
File:COVID-19-23354,uniform,e=15,triangulation,zoom.png
+
<gallery mode="packed" heights=350px>
 +
File:Ircad2,d=1,graded.png
 
</gallery>
 
</gallery>
−
<gallery mode="packed" heights=250px>
+
<gallery mode="packed" heights=350px>
−
File:COVID-19-23354,w=0.1,e=15,suface.png
+
File:Ircad2,d=2,el=1.png
−
File:COVID-19-23354,w=0.1,e=15,triangulation.png
 
−
File:COVID-19-23354,w=0.1,e=15,triangulation,zoom.png
 
 
</gallery>
 
</gallery>
  
−
Commands to generate meshes :
+
Commands to generate meshes:
  
−
'''Uniform with Min-Edge = 15 :''' [https://odu.box.com/s/g1ujcqm76q0oxa0cm9dderp9tf5hqubt Output Mesh]
+
'''Uniform with Delta = 2:''' [https://odu.box.com/s/nfqgcr1j1j6wdnydb9sug8652y9falvc Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m tessellate2d --input ./Medical_Imaging_Data/2D/COVID-19-23354.tif --uniform --min-edge 15 --output ./COVID-19-23354,uniform,e=15.vtk
+
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --delta 2 --threads 6 --output ./Ircad2,d=2.vtk
 
</pre>
 
</pre>
  
−
'''Adaptive with Min-Edge = 15 :''' [https://odu.box.com/s/bf0w2cfh7ww8wsm45e9yfxahiwb1m864 Output Mesh]
+
'''Graded with Delta = 1:''' [https://odu.box.com/s/ofnxslfgijzbqbwqqlvcetm783kqv9uo Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m tessellate2d --input ./Medical_Imaging_Data/2D/COVID-19-23354.tif --min-edge 15 --output ./COVID-19-23354,w=0.1,e=15.vtk
+
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --delta 1 --threads 6 --volume-grading --output ./Ircad2,d=1,graded.vtk
 
</pre>
 
</pre>
  
−
Mesh generated based on the images published at [https://phil.cdc.gov//PHIL_Images/23354/23354.tif ]. For the uniform meshes, the edge-size corresponds to 15 pixels. The adaptive meshes were created by controlling the size of the elements based on the difference in the intensity of the pixels
+
'''Uniform with Delta = 2 and excluded label 1:''' [https://odu.box.com/s/5jaukd6317jdmi8li479h8emknuw0rny Output Mesh]
−
 
 
−
==COVID-19-23311==
 
−
* Input image : Dimensions (2,460x2,460) with spacing (1x1)
 
−
* Uniform with Min-Edge = 20: 47,028 triangles
 
−
* Adaptive with Min-Edge = 20: 34,080 tetrahedra
 
−
 
 
−
<gallery mode="packed" heights=250px>
 
−
File:COVID-19-23311,uniform,e=20,suface.png
 
−
File:COVID-19-23311,uniform,e=20,triangulation.png
 
−
File:COVID-19-23311,uniform,e=20,triangulation,zoom.png
 
−
</gallery>
 
−
<gallery mode="packed" heights=250px>
 
−
File:COVID-19-23311,w=0.1,e=20,suface.png
 
−
File:COVID-19-23311,w=0.1,e=20,triangulation.png
 
−
File:COVID-19-23311,w=0.1,e=20,triangulation,zoom.png
 
−
</gallery>
 
−
 
 
−
Commands to generate meshes :
 
−
 
 
−
'''Uniform with Min-Edge = 20 :''' [https://odu.box.com/s/dkv6271ky0cxvk4lio2bvw6jv9zw5iaf Output Mesh]
 
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m tessellate2d --input ./Medical_Imaging_Data/2D/COVID-19-23311.tif --uniform --min-edge 20 --output ./COVID-19-23311,uniform,e=20.vtk
+
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --exclude-labels 1 --delta 2 --threads 6 --output ./Ircad2,d=2,el=1.vtk
 
</pre>
 
</pre>
  
−
'''Adaptive with Min-Edge = 20 :''' [https://odu.box.com/s/jeqmz2c8dsssl8zujkywl2v3bjaby8gc Output Mesh]
+
==Knee-Char==
−
<pre>
+
* [https://odu.box.com/s/jv3rqazsth3ktd8ipsstzqjl6ryz8naf Input Image]
−
docker run -v $(pwd):/data/ crtc_i2m tessellate2d --input ./Medical_Imaging_Data/2D/COVID-19-23311.tif --min-edge 20 --output ./COVID-19-23311,w=0.1,e=20.vtk
+
* Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1)
−
</pre>
+
* Uniform with Delta = default : 386,869 tetrahedra
−
 
+
* Graded with Delta = default : 274,309 tetrahedra
−
=3D Example Meshes=
 
−
The directory containing the 3D input data is located in the 3D folder of [https://odu.box.com/s/wd0i18giti2zo330y19xhkqu8wjzgf7j Medical_Imaging_Data].
 
−
 
 
−
==Head-Neck==
 
−
* Input image : Dimensions (255x255x229) with spacing (0.976562x0.976562x1.40002)
 
−
* Uniform with Delta = default: 205,416 tetrahedra
 
−
* Uniform with Delta = 1.5: 770,853 tetrahedra
 
  
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
−
File:Head-Neck,d=2.49023.png
+
File:Knee-Char,d=1.19.png
−
File:Head-Neck,d=2.49023,zoom.png
 
 
</gallery>
 
</gallery>
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
−
File:Head-Neck,d=1.5.png
+
File:Knee-Char,d=1.19,graded.png
−
File:Head-Neck,d=1.5,zoom.png
 
 
</gallery>
 
</gallery>
  
−
Commands to generate meshes :
+
Commands to generate meshes:
  
−
'''Uniform with Delta = default :''' [https://odu.box.com/s/adx5yrnxrqia908vzcotqpkpl3dpvttv Output Mesh]
+
'''Uniform with Delta = default :''' [https://odu.box.com/s/q42ekuymr0gy0w882ilcngjfg8l95xvx Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --output ./Head-Neck,d=2.49023.vtk
+
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Knee-Char.mha --output ./Knee-Char,d=1.19.vtk
 
</pre>
 
</pre>
  
−
'''Uniform with Delta = 1.5 :''' [https://odu.box.com/s/pv0ss8s08oucmsfcbaifyx89isgwb041 Output Mesh]
+
'''Graded with Delta = default :''' [https://odu.box.com/s/i788xycxrd11wpxneo4wq3x0ekk9yemm Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --delta 1.5 --output ./Head-Neck,d=1.5.vtk
+
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Knee-Char.mha --volume-grading --output ./Knee-Char,d=1.19,graded.vtk
 
</pre>
 
</pre>
  
 
==Brain-With-Tumor-Case17==
 
==Brain-With-Tumor-Case17==
 +
* [https://odu.box.com/s/ynudkxeozt5j82v1qmoovif10c73taw7 Input Image]
 
* Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
 
* Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
 
* Uniform with Delta = default: 222,540 tetrahedra
 
* Uniform with Delta = default: 222,540 tetrahedra
Line 99: Line 71:
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
 
File:Brain-With-Tumor-Case17,d=1.76001.png
 
File:Brain-With-Tumor-Case17,d=1.76001.png
−
File:Brain-With-Tumor-Case17,d=1.76001,zoom.png
 
 
</gallery>
 
</gallery>
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
 
File:Brain-With-Tumor-Case17,d=1.76001,graded.png
 
File:Brain-With-Tumor-Case17,d=1.76001,graded.png
−
File:Brain-With-Tumor-Case17,d=1.76001,graded,zoom.png
 
 
</gallery>
 
</gallery>
  
−
Commands to generate meshes :
+
Commands to generate meshes:
  
−
'''Uniform with Delta = default :''' [https://odu.box.com/s/5dqgw5pykve4xv2ii30xnkjq5s3maxdl Output Mesh]
+
'''Uniform with Delta = default:''' [https://odu.box.com/s/5dqgw5pykve4xv2ii30xnkjq5s3maxdl Output Mesh]
 
<pre>
 
<pre>
 
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Brain-With-Tumor-Case17.nii --output ./Brain-With-Tumor-Case17,d=1.76001.vtk
 
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Brain-With-Tumor-Case17.nii --output ./Brain-With-Tumor-Case17,d=1.76001.vtk
 
</pre>
 
</pre>
  
−
'''Graded with Delta = default :''' [https://odu.box.com/s/8zlfyepfuzmd8g119eup5n2srxpbqg8s Output Mesh]
+
'''Graded with Delta = default:''' [https://odu.box.com/s/8zlfyepfuzmd8g119eup5n2srxpbqg8s Output Mesh]
 
<pre>
 
<pre>
 
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Brain-With-Tumor-Case17.nii --volume-grading --output ./Brain-With-Tumor-Case17,d=1.76001,graded.vtk
 
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Brain-With-Tumor-Case17.nii --volume-grading --output ./Brain-With-Tumor-Case17,d=1.76001,graded.vtk
 
</pre>
 
</pre>
  
−
==Knee-Char==
+
==Head-Neck==
−
* Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1)
+
* [https://odu.box.com/s/zj492g475bo93kyrd1npmisy2gwdqorj Input Image]
−
* Uniform with Delta = default case: 386,869 tetrahedra
+
* Input image : Dimensions (255x255x229) with spacing (0.976562x0.976562x1.40002)
−
* Graded with Delta = default case: 274,309 tetrahedra
+
* Uniform with Delta = default: 205,510 tetrahedra
 +
* Uniform with Delta = 1.5: 767,393 tetrahedra
  
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
−
File:Knee-Char,d=1.19.png
+
File:Head-Neck,d=2.49023.png
−
File:Knee-Char,d=1.19,zoom.png
 
 
</gallery>
 
</gallery>
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
−
File:Knee-Char,d=1.19,graded.png
+
File:Head-Neck,d=1.5.png
−
File:Knee-Char,d=1.19,graded,zoom.png
 
 
</gallery>
 
</gallery>
  
−
Commands to generate meshes :
+
Commands to generate meshes:
  
−
'''Uniform with Delta = default :''' [https://odu.box.com/s/q42ekuymr0gy0w882ilcngjfg8l95xvx Output Mesh]
+
'''Uniform with Delta = default:''' [https://odu.box.com/s/zoi0em9twv0mgt2d1244yujtkd3nit3e Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --output ./Knee-Char,d=1.19.vtk
+
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --output ./Head-Neck,d=2.49023.vtk
 
</pre>
 
</pre>
  
−
'''Graded with Delta = default :''' [https://odu.box.com/s/i788xycxrd11wpxneo4wq3x0ekk9yemm Output Mesh]
+
'''Uniform with Delta = 1.5:''' [https://odu.box.com/s/jo4cwfrn1bvslocv9b11m0i9dhxyvdrc Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --volume-grading --output ./Knee-Char,d=1.19,graded.vtk
+
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --delta 1.5 --output ./Head-Neck,d=1.5.vtk
−
</pre>
 
−
 
 
−
==Ircad2==
 
−
* Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002)
 
−
* Uniform with Delta = 2 case: 5,031,442 tetrahedra
 
−
* Graded with Delta = 1 case: 6,072,751 tetrahedra
 
−
 
 
−
<gallery mode="packed" heights=350px>
 
−
File:Ircad2,d=2.png
 
−
File:Ircad2,d=2,zoom.png
 
−
</gallery>
 
−
<gallery mode="packed" heights=350px>
 
−
File:Ircad2,d=1,graded.png
 
−
File:Ircad2,d=1,graded,zoom.png
 
−
</gallery>
 
−
 
 
−
Commands to generate meshes :
 
−
 
 
−
'''Uniform with Delta = 2 :''' [https://odu.box.com/s/nfqgcr1j1j6wdnydb9sug8652y9falvc Output Mesh]
 
−
<pre>
 
−
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --delta 2 --threads 4 --output ./Ircad2,d=2.vtk
 
−
</pre>
 
−
 
 
−
'''Graded with Delta = 1 :''' [https://odu.box.com/s/ofnxslfgijzbqbwqqlvcetm783kqv9uo Output Mesh]
 
−
<pre>
 
−
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --delta 1 --threads 4 --volume-grading --output ./Ircad2,d=1,graded.vtk
 
 
</pre>
 
</pre>

Latest revision as of 15:57, 2 June 2020

3D Example Meshes

The directory containing the 3D input data is located in the 3D folder of Medical_Imaging_Data.

Ircad2

  • Input Image
  • Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002)
  • Uniform with Delta = 2: 5,031,442 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
  • Graded with Delta = 1: 6,072,751 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
  • Uniform with Delta = 2 and excluded label 1: 1,941,468 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
  • Ircad2,d=2.png
  • Ircad2,d=1,graded.png
  • Ircad2,d=2,el=1.png

Commands to generate meshes:

Uniform with Delta = 2: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --delta 2 --threads 6 --output ./Ircad2,d=2.vtk

Graded with Delta = 1: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --delta 1 --threads 6 --volume-grading --output ./Ircad2,d=1,graded.vtk

Uniform with Delta = 2 and excluded label 1: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Ircad2.nrrd --exclude-labels 1 --delta 2 --threads 6 --output ./Ircad2,d=2,el=1.vtk

Knee-Char

  • Input Image
  • Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1)
  • Uniform with Delta = default : 386,869 tetrahedra
  • Graded with Delta = default : 274,309 tetrahedra
  • Knee-Char,d=1.19.png
  • Knee-Char,d=1.19,graded.png

Commands to generate meshes:

Uniform with Delta = default : Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Knee-Char.mha --output ./Knee-Char,d=1.19.vtk

Graded with Delta = default : Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Knee-Char.mha --volume-grading --output ./Knee-Char,d=1.19,graded.vtk

Brain-With-Tumor-Case17

  • Input Image
  • Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
  • Uniform with Delta = default: 222,540 tetrahedra
  • Graded with Delta = default: 94,383 tetrahedra
  • Brain-With-Tumor-Case17,d=1.76001.png
  • Brain-With-Tumor-Case17,d=1.76001,graded.png

Commands to generate meshes:

Uniform with Delta = default: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Brain-With-Tumor-Case17.nii --output ./Brain-With-Tumor-Case17,d=1.76001.vtk

Graded with Delta = default: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Brain-With-Tumor-Case17.nii --volume-grading --output ./Brain-With-Tumor-Case17,d=1.76001,graded.vtk

Head-Neck

  • Input Image
  • Input image : Dimensions (255x255x229) with spacing (0.976562x0.976562x1.40002)
  • Uniform with Delta = default: 205,510 tetrahedra
  • Uniform with Delta = 1.5: 767,393 tetrahedra
  • Head-Neck,d=2.49023.png
  • Head-Neck,d=1.5.png

Commands to generate meshes:

Uniform with Delta = default: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --output ./Head-Neck,d=2.49023.vtk

Uniform with Delta = 1.5: Output Mesh 

docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/Head-Neck.mha --delta 1.5 --output ./Head-Neck,d=1.5.vtk
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