Difference between revisions of "Medical Imaging Example Meshes"
From crtc.cs.odu.edu
Spyridon97 (talk | contribs) (→Brain-With-Tumor-Case17) |
Spyridon97 (talk | contribs) |
||
| (122 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
__TOC__ | __TOC__ | ||
| − | The directory containing the input data is located in the 3D folder of [https://odu.box.com/s/ | + | =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]. | ||
| − | = | + | ==Ircad2== |
| − | * Input image : Dimensions ( | + | * [https://odu.box.com/s/1ef11ry4yik5mny62dz6zyd9obqb540i Input Image] |
| − | * Uniform with Delta = | + | * Input image : Dimensions (512x512x219) with spacing (0.976562x0.976562x1.40002) |
| − | * Uniform with Delta = 1 | + | * 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: | + | File:Ircad2,d=2.png |
| − | File: | + | </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: | + | File:Ircad2,d=2,el=1.png |
| − | |||
</gallery> | </gallery> | ||
| − | Commands to generate meshes : | + | Commands to generate meshes: |
| − | '''Uniform with Delta = | + | '''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/ | + | 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> | </pre> | ||
| − | '''Uniform with Delta = 1 | + | '''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/ | + | 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== |
| − | * Input image : Dimensions ( | + | * [https://odu.box.com/s/jv3rqazsth3ktd8ipsstzqjl6ryz8naf Input Image] |
| − | * Uniform with Delta = default: | + | * Input image : Dimensions (512x512x119) with spacing (0.27734x0.27734x1) |
| − | * Graded with Delta = default: | + | * 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: | + | File:Knee-Char,d=1.19.png |
| − | |||
</gallery> | </gallery> | ||
<gallery mode="packed" heights=350px> | <gallery mode="packed" heights=350px> | ||
| − | File: | + | File:Knee-Char,d=1.19,graded.png |
| − | |||
</gallery> | </gallery> | ||
| − | Commands to generate meshes : | + | Commands to generate meshes: |
| − | '''Uniform with Delta = default :''' [https://odu.box.com/s/ | + | '''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/ | + | 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 with Delta = default :''' [https://odu.box.com/s/ | + | '''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/ | + | 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== |
| − | * Input image : Dimensions ( | + | * [https://odu.box.com/s/ynudkxeozt5j82v1qmoovif10c73taw7 Input Image] |
| − | * Uniform with Delta = default | + | * Input image : Dimensions (448x512x176) with spacing (0.488281x0.488281x1) |
| − | * Graded with Delta = default | + | * 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: | + | File:Brain-With-Tumor-Case17,d=1.76001.png |
| − | |||
</gallery> | </gallery> | ||
<gallery mode="packed" heights=350px> | <gallery mode="packed" heights=350px> | ||
| − | File: | + | File:Brain-With-Tumor-Case17,d=1.76001,graded.png |
| − | |||
</gallery> | </gallery> | ||
| − | Commands to generate meshes : | + | Commands to generate meshes: |
| − | '''Uniform :''' [https://odu.box.com/s/ | + | '''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/ | + | 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/ | + | '''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/ | + | 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> | ||
| − | = | + | ==Head-Neck== |
| − | * Input image : Dimensions ( | + | * [https://odu.box.com/s/zj492g475bo93kyrd1npmisy2gwdqorj Input Image] |
| − | * Uniform with Delta = | + | * 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: | + | File:Head-Neck,d=2.49023.png |
| − | |||
</gallery> | </gallery> | ||
<gallery mode="packed" heights=350px> | <gallery mode="packed" heights=350px> | ||
| − | File: | + | File:Head-Neck,d=1.5.png |
| − | |||
</gallery> | </gallery> | ||
| − | Commands to generate meshes : | + | Commands to generate meshes: |
| − | '''Uniform with Delta = | + | '''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/ | + | 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> | ||
| − | ''' | + | '''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/ | + | 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)
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
