Difference between revisions of "Medical Imaging Example Meshes"

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=3D Example Meshes=
 
=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].
+
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-Spike-Glycoprotein-6vsb==
+
==Ircad2==
−
* Input image : Dimensions (220x223x314) with spacing (0.551042x0.551042x0.551042)
+
* [https://odu.box.com/s/1ef11ry4yik5mny62dz6zyd9obqb540i Input Image]
−
* Uniform with Delta = 0.4: 5,731,833 tetrahedra
+
* Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002)
−
* Graded with Delta = 0.4: 3,794,223 tetrahedra
+
* 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-Spike-Glycoprotein-6vsb,d=0.4.png
+
File:Ircad2,d=2.png
−
File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4,clip.png
 
−
File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4,clip,zoom.png
 
 
</gallery>
 
</gallery>
−
<gallery mode="packed" heights=250px>
 
−
File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4,graded.png
 
−
File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4,graded,clip.png
 
−
File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4,graded,clip,zoom.png
 
−
</gallery>
 
−
 
−
Commands to generate meshes :
 
−
 
−
'''Uniform with Delta = 0.4:''' [https://odu.box.com/s/wth64bzfotibrwv3t25kn2oyzo0dqntm Output Mesh]
 
−
<pre>
 
−
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/COVID-19-Spike-Glycoprotein-6vsb.nrrd --delta 0.4 --output ./COVID-19-Spike-Glycoprotein-6vsb,d=0.4.vtk
 
−
</pre>
 
−
 
−
'''Graded with Delta = 0.4:''' [https://odu.box.com/s/2kn1ovwpa6jarj8wssmeqz2y5zc19fc2 Output Mesh]
 
−
<pre>
 
−
docker run -v $(pwd):/data/ crtc_i2m tessellate3d --input ./Medical_Imaging_Data/3D/COVID-19-Spike-Glycoprotein-6vsb.nrrd --delta 0.4 --volume-grading --output ./COVID-19-Spike-Glycoprotein-6vsb,d=0.4,graded.vtk
 
−
</pre>
 
−
 
−
A tetrahedral mesh of the surface of the COVID-19 spike glycoprotein. Bioassembly data was retrieved from molecule [https://www.rcsb.org/structure/6vsb 6vsb] from the [https://www.rcsb.org/ Protein Data Bank]
 
−
 
−
==Head-Neck==
 
−
* 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
 
−
 
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
−
File:Head-Neck,d=2.49023.png
+
File:Ircad2,d=1,graded.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:Ircad2,d=2,el=1.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/zoi0em9twv0mgt2d1244yujtkd3nit3e Output Mesh]
+
'''Uniform with Delta = 2:''' [https://odu.box.com/s/nfqgcr1j1j6wdnydb9sug8652y9falvc 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/Ircad2.nrrd --delta 2 --threads 6 --output ./Ircad2,d=2.vtk
 
</pre>
 
</pre>
  
−
'''Uniform with Delta = 1.5 :''' [https://odu.box.com/s/jo4cwfrn1bvslocv9b11m0i9dhxyvdrc Output Mesh]
+
'''Graded with Delta = 1:''' [https://odu.box.com/s/ofnxslfgijzbqbwqqlvcetm783kqv9uo 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/Ircad2.nrrd --delta 1 --threads 6 --volume-grading --output ./Ircad2,d=1,graded.vtk
−
</pre>
 
−
 
 
−
==Brain-With-Tumor-Case17==
 
−
* Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
 
−
* Uniform with Delta = default: 222,540 tetrahedra
 
−
* Graded with Delta = default: 94,383 tetrahedra
 
−
 
 
−
<gallery mode="packed" heights=350px>
 
−
File:Brain-With-Tumor-Case17,d=1.76001.png
 
−
File:Brain-With-Tumor-Case17,d=1.76001,zoom.png
 
−
</gallery>
 
−
<gallery mode="packed" heights=350px>
 
−
File:Brain-With-Tumor-Case17,d=1.76001,graded.png
 
−
File:Brain-With-Tumor-Case17,d=1.76001,graded,zoom.png
 
−
</gallery>
 
−
 
 
−
Commands to generate meshes :
 
−
 
 
−
'''Uniform with Delta = default :''' [https://odu.box.com/s/5dqgw5pykve4xv2ii30xnkjq5s3maxdl Output Mesh]
 
−
<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
 
 
</pre>
 
</pre>
  
−
'''Graded with Delta = default :''' [https://odu.box.com/s/8zlfyepfuzmd8g119eup5n2srxpbqg8s Output Mesh]
+
'''Uniform with Delta = 2 and excluded label 1:''' [https://odu.box.com/s/5jaukd6317jdmi8li479h8emknuw0rny 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/Ircad2.nrrd --exclude-labels 1 --delta 2 --threads 6 --output ./Ircad2,d=2,el=1.vtk
 
</pre>
 
</pre>
  
 
==Knee-Char==
 
==Knee-Char==
 +
* [https://odu.box.com/s/jv3rqazsth3ktd8ipsstzqjl6ryz8naf Input Image]
 
* Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1)
 
* Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1)
 
* Uniform with Delta = default : 386,869 tetrahedra
 
* Uniform with Delta = default : 386,869 tetrahedra
Line 93: Line 46:
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
 
File:Knee-Char,d=1.19.png
 
File:Knee-Char,d=1.19.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:Knee-Char,d=1.19,graded.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/q42ekuymr0gy0w882ilcngjfg8l95xvx Output Mesh]
Line 112: Line 63:
 
</pre>
 
</pre>
  
−
==Ircad2==
+
==Brain-With-Tumor-Case17==
−
* Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002)
+
* [https://odu.box.com/s/ynudkxeozt5j82v1qmoovif10c73taw7 Input Image]
−
* Uniform with Delta = 2: 5,031,442 tetrahedra (#elements for each execution might differ due to the usage of more than one thread)
+
* Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
−
* 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 = default: 222,540 tetrahedra
 +
* Graded with Delta = default: 94,383 tetrahedra
  
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
−
File:Ircad2,d=2.png
+
File:Brain-With-Tumor-Case17,d=1.76001.png
−
File:Ircad2,d=2,zoom.png
 
 
</gallery>
 
</gallery>
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
−
File:Ircad2,d=1,graded.png
+
File:Brain-With-Tumor-Case17,d=1.76001,graded.png
−
File:Ircad2,d=1,graded,zoom.png
 
 
</gallery>
 
</gallery>
  
−
Commands to generate meshes :
+
Commands to generate meshes:
  
−
'''Uniform with Delta = 2 :''' [https://odu.box.com/s/nfqgcr1j1j6wdnydb9sug8652y9falvc 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/Ircad2.nrrd --delta 2 --threads 6 --output ./Ircad2,d=2.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 = 1 :''' [https://odu.box.com/s/ofnxslfgijzbqbwqqlvcetm783kqv9uo 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/Ircad2.nrrd --delta 1 --threads 6 --volume-grading --output ./Ircad2,d=1,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>
  
−
=2D Example Meshes=
+
==Head-Neck==
−
The directory containing the 2D input data is located in the 2D folder of [https://odu.box.com/s/wd0i18giti2zo330y19xhkqu8wjzgf7j Medical_Imaging_Data].
+
* [https://odu.box.com/s/zj492g475bo93kyrd1npmisy2gwdqorj 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
  
−
==COVID-19-23354==
+
<gallery mode="packed" heights=350px>
−
* Input image : Dimensions (3,000x2,000) with spacing (1x1)
+
File:Head-Neck,d=2.49023.png
−
* Uniform with Min-Edge = 15: 82,981 triangles
 
−
* Adaptive with Min-Edge = 15: 67,920 triangles
 
−
 
 
−
<gallery mode="packed" heights=250px>
 
−
File:COVID-19-23354,uniform,e=15,suface.png
 
−
File:COVID-19-23354,uniform,e=15,triangulation.png
 
−
File:COVID-19-23354,uniform,e=15,triangulation,zoom.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:Head-Neck,d=1.5.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 = default:''' [https://odu.box.com/s/zoi0em9twv0mgt2d1244yujtkd3nit3e 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/Head-Neck.mha --output ./Head-Neck,d=2.49023.vtk
 
</pre>
 
</pre>
  
−
'''Adaptive with Min-Edge = 15:''' [https://odu.box.com/s/bf0w2cfh7ww8wsm45e9yfxahiwb1m864 Output Mesh]
+
'''Uniform with Delta = 1.5:''' [https://odu.box.com/s/jo4cwfrn1bvslocv9b11m0i9dhxyvdrc 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/Head-Neck.mha --delta 1.5 --output ./Head-Neck,d=1.5.vtk
 
</pre>
 
</pre>
−
 
−
Mesh generated based on the images published at [https://phil.cdc.gov//PHIL_Images/23354/23354.tif Centers for Disease Control and Prevention]. 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.
 
−
 
−
==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>
 
−
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
 
−
</pre>
 
−
 
−
'''Adaptive with Min-Edge = 20:''' [https://odu.box.com/s/jeqmz2c8dsssl8zujkywl2v3bjaby8gc Output Mesh]
 
−
<pre>
 
−
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
 
−
</pre>
 
−
 
−
Mesh generated based on the images published at [https://phil.cdc.gov//PHIL_Images/23311/23311.tif Centers for Disease Control and Prevention]. For the uniform meshes, the edge-size corresponds to 20 pixels. The adaptive meshes were created by controlling the size of the elements based on the difference in the intensity of the pixels.
 

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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