Difference between revisions of "Medical Imaging Example Meshes"

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__TOC__
 
__TOC__
  
−
The directory containing the input data is [https://odu.box.com/s/wd0i18giti2zo330y19xhkqu8wjzgf7j Medical_Imaging_Data].
+
=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].
  
−
=Head-Neck=
+
==Ircad2==
−
* Input image : Dimensions (255x255x229) with spacing (0.976562x0.976562x1.40002)
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* [https://odu.box.com/s/1ef11ry4yik5mny62dz6zyd9obqb540i Input Image]
−
* Delta = 2.49023 (Default) case: 205,416 tetrahedra
+
* Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002)
−
* Delta = 1.5 case: 770,853 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)
  
−
[[File:Head-Neck,d=2.49023.png|500px|Head-Neck,d=2.49023.png]]
 
−
[[File:Head-Neck,d=2.49023,zoom.png|500px|Head-Neck,d=2.49023,zoom.png]]
 
−
[[File:Head-Neck,d=1.5.png|500px|Head-Neck,d=1.5.png]]
 
−
[[File:Head-Neck,d=1.5,zoom.png|500px|Head-Neck,d=1.5,zoom.png]]
 
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
 +
File:Ircad2,d=2.png
 +
</gallery>
 +
<gallery mode="packed" heights=350px>
 +
File:Ircad2,d=1,graded.png
 
</gallery>
 
</gallery>
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
 +
File:Ircad2,d=2,el=1.png
 
</gallery>
 
</gallery>
  
−
Commands to generate meshes :
+
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 6 --output ./Ircad2,d=2.vtk
 +
</pre>
  
−
'''Delta = 2.49023 :''' [ Output Mesh]
+
'''Graded with Delta = 1:''' [https://odu.box.com/s/ofnxslfgijzbqbwqqlvcetm783kqv9uo Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/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 1 --threads 6 --volume-grading --output ./Ircad2,d=1,graded.vtk
 
</pre>
 
</pre>
  
−
'''Delta = 1.5 :''' [ 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 podm3d --input ./Medical_Imaging_Data/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 --exclude-labels 1 --delta 2 --threads 6 --output ./Ircad2,d=2,el=1.vtk
 
</pre>
 
</pre>
  
−
=Brain-With-Tumor-Case17=
+
==Knee-Char==
−
* Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
+
* [https://odu.box.com/s/jv3rqazsth3ktd8ipsstzqjl6ryz8naf Input Image]
−
* Uniform with Delta = 1.76001 (Default) case: 222,540 tetrahedra
+
* Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1)
−
* Graded with Delta = 1.76001 (Default) case: 94,383 tetrahedra
+
* Uniform with Delta = default : 386,869 tetrahedra
 +
* Graded with Delta = default : 274,309 tetrahedra
  
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
−
File:Brain-With-Tumor-Case17,d=1.76001.png
+
File:Knee-Char,d=1.19.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:Knee-Char,d=1.19,graded.png
−
File:Brain-With-Tumor-Case17,d=1.76001,graded,zoom.png
 
 
</gallery>
 
</gallery>
  
−
Commands to generate meshes :
+
Commands to generate meshes:
  
−
'''Uniform :''' [https://odu.box.com/s/5dqgw5pykve4xv2ii30xnkjq5s3maxdl Output Mesh]
+
'''Uniform with Delta = default :''' [https://odu.box.com/s/q42ekuymr0gy0w882ilcngjfg8l95xvx Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/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/Knee-Char.mha --output ./Knee-Char,d=1.19.vtk
 
</pre>
 
</pre>
  
−
'''Graded :''' [https://odu.box.com/s/8zlfyepfuzmd8g119eup5n2srxpbqg8s Output Mesh]
+
'''Graded with Delta = default :''' [https://odu.box.com/s/i788xycxrd11wpxneo4wq3x0ekk9yemm Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/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/Knee-Char.mha --volume-grading --output ./Knee-Char,d=1.19,graded.vtk
 
</pre>
 
</pre>
  
−
=Knee-Char=
+
==Brain-With-Tumor-Case17==
−
* Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1)
+
* [https://odu.box.com/s/ynudkxeozt5j82v1qmoovif10c73taw7 Input Image]
−
* Uniform with Delta = 1.19 (Default) case: 386,869 tetrahedra
+
* Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
−
* Graded with Delta = 1.19 (Default) case: 274,309 tetrahedra
+
* 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:Knee-Char,d=1.19.png
+
File:Brain-With-Tumor-Case17,d=1.76001.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:Brain-With-Tumor-Case17,d=1.76001,graded.png
−
File:Knee-Char,d=1.19,graded,zoom.png
 
 
</gallery>
 
</gallery>
  
−
Commands to generate meshes :
+
Commands to generate meshes:
  
−
'''Uniform :''' [https://odu.box.com/s/q42ekuymr0gy0w882ilcngjfg8l95xvx Output Mesh]
+
'''Uniform with Delta = default:''' [https://odu.box.com/s/5dqgw5pykve4xv2ii30xnkjq5s3maxdl Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Head-Neck.mha --output ./Knee-Char,d=1.19.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 :''' [https://odu.box.com/s/i788xycxrd11wpxneo4wq3x0ekk9yemm Output Mesh]
+
'''Graded with Delta = default:''' [https://odu.box.com/s/8zlfyepfuzmd8g119eup5n2srxpbqg8s Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/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/Brain-With-Tumor-Case17.nii --volume-grading --output ./Brain-With-Tumor-Case17,d=1.76001,graded.vtk
 
</pre>
 
</pre>
  
−
=Ircad2-Removed-Tissues=  
+
==Head-Neck==
−
* Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002)
+
* [https://odu.box.com/s/zj492g475bo93kyrd1npmisy2gwdqorj Input Image]
−
* Uniform with Delta = 4.92032 (Default) case: 16,685,902 tetrahedra
+
* Input image : Dimensions (255x255x229) with spacing (0.976562x0.976562x1.40002)
−
* Graded with Delta = 4.92032 (Default) case: 14,462,494 tetrahedra
+
* Uniform with Delta = default: 205,510 tetrahedra
 +
* Uniform with Delta = 1.5: 767,393 tetrahedra
  
−
[[File:Ircad2-Removed-Tissues,d=4.92032.png|500px|Ircad2-Removed-Tissues,d=4.92032.png]]
 
−
[[File:Ircad2-Removed-Tissues,d=4.92032,graded.png|500px|Ircad2-Removed-Tissues,d=4.92032,graded.png]]
 
 
<gallery mode="packed" heights=350px>
 
<gallery mode="packed" heights=350px>
 +
File:Head-Neck,d=2.49023.png
 +
</gallery>
 +
<gallery mode="packed" heights=350px>
 +
File:Head-Neck,d=1.5.png
 
</gallery>
 
</gallery>
  
−
Commands to generate meshes :
+
Commands to generate meshes:
  
−
'''Uniform :''' [ Output Mesh]
+
'''Uniform with Delta = default:''' [https://odu.box.com/s/zoi0em9twv0mgt2d1244yujtkd3nit3e Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Ircad2-Removed-Tissues.nrrd --output ./Ircad2-Removed-Tissues,d=4.92032.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  :''' [ Output Mesh]
+
'''Uniform with Delta = 1.5:''' [https://odu.box.com/s/jo4cwfrn1bvslocv9b11m0i9dhxyvdrc Output Mesh]
 
<pre>
 
<pre>
−
docker run -v $(pwd):/data/ crtc_i2m podm3d --input ./Medical_Imaging_Data/Ircad2-Removed-Tissues.nrrd --volume-grading --output ./Ircad2-Removed-Tissues,d=4.92032,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>
 
</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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