Medical Imaging Example Meshes: Difference between revisions

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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)
* [https://odu.box.com/s/1ef11ry4yik5mny62dz6zyd9obqb540i Input Image]
* Delta = 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)


<gallery mode="packed" heights=350px>
<gallery mode="packed" heights=350px>
File:Head-Neck,d=2.49023.png
File:Ircad2,d=2.png
File:Head-Neck,d=2.49023,zoom.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: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:


'''Delta = default :''' [https://odu.box.com/s/adx5yrnxrqia908vzcotqpkpl3dpvttv Output Mesh]
'''Uniform with Delta = 2:''' [https://odu.box.com/s/nfqgcr1j1j6wdnydb9sug8652y9falvc 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 2 --threads 6 --output ./Ircad2,d=2.vtk
</pre>
</pre>


'''Delta = 1.5 :''' [https://odu.box.com/s/pv0ss8s08oucmsfcbaifyx89isgwb041 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 --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>
</pre>


=Brain-With-Tumor-Case17=
'''Uniform with Delta = 2 and excluded label 1:''' [https://odu.box.com/s/5jaukd6317jdmi8li479h8emknuw0rny Output Mesh]
* Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
<pre>
* Uniform with Delta = default case: 222,540 tetrahedra
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
* Graded with Delta = default case: 94,383 tetrahedra
</pre>
 
==Knee-Char==
* [https://odu.box.com/s/jv3rqazsth3ktd8ipsstzqjl6ryz8naf 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


<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 = default case: 386,869 tetrahedra
* Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1)
* Graded with Delta = 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=  
==Head-Neck==
* Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002)
* [https://odu.box.com/s/zj492g475bo93kyrd1npmisy2gwdqorj Input Image]
* Uniform with Delta = 2 case: 5,031,442 tetrahedra
* Input image : Dimensions (255x255x229) with spacing (0.976562x0.976562x1.40002)
* Graded with Delta = 1 case: 6,072,751 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:Ircad2,d=2.png|500px|Ircad2,d=2.png]]
File:Head-Neck,d=2.49023.png
[[File:Ircad2,d=2,zoom.png|500px|Ircad2,d=2,zoom.png]]
</gallery>
</gallery>
<gallery mode="packed" heights=350px>
<gallery mode="packed" heights=350px>
[[File:Ircad2,d=1,graded.png|500px|Ircad2,d=1,graded.png]]
File:Head-Neck,d=1.5.png
[[File:Ircad2,d=1,graded,zoom.png|500px|Ircad2,d=1,graded,zoom.png]]
</gallery>
</gallery>


Commands to generate meshes :
Commands to generate meshes:


'''Uniform :''' [https://odu.box.com/s/nfqgcr1j1j6wdnydb9sug8652y9falvc 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.nrrd --delta 2 --output ./Ircad2,d=2.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  :''' [https://odu.box.com/s/ofnxslfgijzbqbwqqlvcetm783kqv9uo 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.nrrd --delta 1 --volume-grading --output ./Ircad2,d=1,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 11:57, 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)

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

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

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

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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