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| The directory containing the 3D input data is located in the 3D folder of [https://odu.box.com/s/olefferrnksu2nmerbfvbvsz2u4abbdw 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]. |
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| ==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> | | <gallery mode="packed" heights=350px> |
| File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4,graded.png | | File:Ircad2,d=1,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> | | </gallery> |
| | | <gallery mode="packed" heights=350px> |
| Commands to generate meshes:
| | File:Ircad2,d=2,el=1.png |
| | |
| '''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>
| |
| | |
| Uniform and graded tetrahedral meshes of the surface of the <b>COVID-19</b> spike glycoprotein. The middle and right meshes are slices. Biological assembly data was retrieved from molecule [https://www.rcsb.org/structure/6vsb 6vsb] from the [https://www.rcsb.org/ Protein Data Bank].
| |
| | |
| ==COVID-19-Spike-Glycoprotein-6vsb==
| |
| * Input image : Dimensions (220x223x314) with spacing (0.551042x0.551042x0.551042)
| |
| * Uniform with Delta = 0.4: 5,731,833 tetrahedra
| |
| * Graded with Delta = 0.4: 3,794,223 tetrahedra
| |
| | |
| <gallery mode="packed" heights=250px> | |
| File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4.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 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> | | </gallery> |
|
| |
|
| Commands to generate meshes: | | Commands to generate meshes: |
|
| |
|
| '''Uniform with Delta = 0.4:''' [https://odu.box.com/s/wth64bzfotibrwv3t25kn2oyzo0dqntm 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/COVID-19-Spike-Glycoprotein-6vsb.nrrd --delta 0.4 --output ./COVID-19-Spike-Glycoprotein-6vsb,d=0.4.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> |
|
| |
|
| '''Graded with Delta = 0.4:''' [https://odu.box.com/s/2kn1ovwpa6jarj8wssmeqz2y5zc19fc2 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/COVID-19-Spike-Glycoprotein-6vsb.nrrd --delta 0.4 --volume-grading --output ./COVID-19-Spike-Glycoprotein-6vsb,d=0.4,graded.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> |
|
| |
|
| Uniform and graded tetrahedral meshes of the surface of the <b>COVID-19</b> spike glycoprotein. The middle and right meshes are slices. Biological assembly data was retrieved from molecule [https://www.rcsb.org/structure/6vsb 6vsb] from the [https://www.rcsb.org/ Protein Data Bank].
| | '''Uniform with Delta = 2 and excluded label 1:''' [https://odu.box.com/s/5jaukd6317jdmi8li479h8emknuw0rny Output Mesh] |
| | |
| ==COVID-19-Spike-Glycoprotein-6vsb==
| |
| * Input image : Dimensions (220x223x314) with spacing (0.551042x0.551042x0.551042)
| |
| * Uniform with Delta = 0.4: 5,731,833 tetrahedra
| |
| * Graded with Delta = 0.4: 3,794,223 tetrahedra
| |
| | |
| <gallery mode="packed" heights=250px>
| |
| File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4.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 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> | | <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 | | 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> |
|
| |
|
| '''Graded with Delta = 0.4:''' [https://odu.box.com/s/2kn1ovwpa6jarj8wssmeqz2y5zc19fc2 Output Mesh]
| | ==Knee-Char== |
| <pre>
| | * [https://odu.box.com/s/jv3rqazsth3ktd8ipsstzqjl6ryz8naf Input Image] |
| 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
| | * Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1) |
| </pre>
| | * Uniform with Delta = default : 386,869 tetrahedra |
| | | * Graded with Delta = default : 274,309 tetrahedra |
| Uniform and graded tetrahedral meshes of the surface of the <b>COVID-19</b> spike glycoprotein. The middle and right meshes are slices. Biological assembly data was retrieved from molecule [https://www.rcsb.org/structure/6vsb 6vsb] from the [https://www.rcsb.org/ Protein Data Bank].
| |
| | |
| ==COVID-19-Spike-Glycoprotein-6vsb== | |
| * Input image : Dimensions (220x223x314) with spacing (0.551042x0.551042x0.551042)
| |
| * Uniform with Delta = 0.4: 5,731,833 tetrahedra | |
| * Graded with Delta = 0.4: 3,794,223 tetrahedra
| |
| | |
| <gallery mode="packed" heights=250px>
| |
| File:COVID-19-Spike-Glycoprotein-6vsb,d=0.4.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 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>
| |
| | |
| Uniform and graded tetrahedral meshes of the surface of the <b>COVID-19</b> spike glycoprotein. The middle and right meshes are slices. Biological assembly 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: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/zoi0em9twv0mgt2d1244yujtkd3nit3e 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/jo4cwfrn1bvslocv9b11m0i9dhxyvdrc 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 157: |
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> |
|
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|
| Line 176: |
Line 88: |
| </pre> | | </pre> |
|
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|
| ==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 : 386,869 tetrahedra | | * Input image : Dimensions (255x255x229) with spacing (0.976562x0.976562x1.40002) |
| * Graded with Delta = default : 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/Knee-Char.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/Knee-Char.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: 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)
| |
| | |
| <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 6 --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 6 --volume-grading --output ./Ircad2,d=1,graded.vtk
| |
| </pre>
| |
| | |
| =2D Example Meshes=
| |
| The directory containing the 2D input data is located in the 2D folder of [https://odu.box.com/s/olefferrnksu2nmerbfvbvsz2u4abbdw Medical_Imaging_Data].
| |
| | |
| ==COVID-19-23354==
| |
| * Input image : Dimensions (3,000x2,000) with spacing (1x1)
| |
| * 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 mode="packed" heights=250px>
| |
| File:COVID-19-23354,w=0.1,e=15,suface.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>
| |
| | |
| Commands to generate meshes:
| |
| | |
| '''Uniform with Min-Edge = 15:''' [https://odu.box.com/s/g1ujcqm76q0oxa0cm9dderp9tf5hqubt Output Mesh]
| |
| <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
| |
| </pre> | | </pre> |
|
| |
| '''Adaptive with Min-Edge = 15:''' [https://odu.box.com/s/bf0w2cfh7ww8wsm45e9yfxahiwb1m864 Output Mesh]
| |
| <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
| |
| </pre>
| |
|
| |
| Mesh generated based on the image [https://phil.cdc.gov//PHIL_Images/23354/23354.tif 23354] retrieved from the [https://www.cdc.gov/media/subtopic/images.htm 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
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| 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 image [https://phil.cdc.gov//PHIL_Images/23311/23311.tif 23311] retrieved from the [https://www.cdc.gov/media/subtopic/images.htm 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.
| |
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
