Difference between revisions of "PREDICT-HD Longitudinal Shape Analysis"
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<gallery> | <gallery> | ||
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]] | Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]] | ||
| + | Image:Left_right_putamen_50406.gif|Evolution of left/right putamen | ||
| + | Image:Putamen_volume_estimated_from_shape_regression.png|Volume of left/right putamen extracted from continuous shape model | ||
</gallery> | </gallery> | ||
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<div style="width: 27%; float: left; padding-right: 3%;"> | <div style="width: 27%; float: left; padding-right: 3%;"> | ||
<h3>Progress</h3> | <h3>Progress</h3> | ||
| − | * | + | * Deformetrica built locally with VTK5. |
| + | * Shape modeling looks good with improved labeling approach | ||
| + | * Code Sharing Plan | ||
| + | ** Source code sharing on a shared point for effective collaboration | ||
| + | ** VTK6 Compatibility (Deformetrica) | ||
| + | ** ITK3/4 Compatibility (ShapeWork) | ||
| + | * Focus area in Statistical Modeling | ||
| + | |||
</div> | </div> | ||
</div> | </div> | ||
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Saving to: 'fftw-3.3.4.tar.gz' | Saving to: 'fftw-3.3.4.tar.gz' | ||
| − | 100%[==================================================================================================================================================>] 3,940,427 4.44MB/s in 0.8s | + | 100%[==================================================================================================================================================>] |
| + | 3,940,427 4.44MB/s in 0.8s | ||
2015-01-06 14:27:59 (4.44 MB/s) - 'fftw-3.3.4.tar.gz' saved [3940427/3940427] | 2015-01-06 14:27:59 (4.44 MB/s) - 'fftw-3.3.4.tar.gz' saved [3940427/3940427] | ||
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$ make install | $ make install | ||
</pre> | </pre> | ||
| + | :* Build deformetrica | ||
| + | <pre> | ||
| + | $ cmake -D ITK_DIR=/Shared/sinapse/sharedopt/UtahShapeTools/ITK4/build/ -D VTK_DIR=/Shared/sinapse/scratch/eunyokim/src/NamicExternal/build_Mac_201410/VTK-build/ ../app | ||
| + | VTK 6.2 is used. | ||
| + | CUDA_TOOLKIT_ROOT_DIR not found or specified | ||
| + | -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) | ||
| + | CUDA was not found. | ||
| + | Deformetrica will be compiled without Cuda | ||
| + | -- Configuring done | ||
| + | -- Generating done | ||
| + | -- Build files have been written to: /Shared/sinapse/sharedopt/UtahShapeTools/deformetrica-2.1/deformetrica/bin | ||
| + | </pre> | ||
| + | :* build | ||
| + | <pre> | ||
| + | $ make | ||
| + | ... ... | ||
| + | Linking CXX executable sparseMatching2 | ||
| + | Linking CXX executable sparseMatching3 | ||
| + | [100%] [100%] Built target sparseMatching3 | ||
| + | Built target sparseMatching2 | ||
| + | </pre> | ||
| + | |||
| + | |||
<h4> ShapeWork Installation </h4> | <h4> ShapeWork Installation </h4> | ||
Latest revision as of 16:26, 9 January 2015
Home < PREDICT-HD Longitudinal Shape Analysis
Evolution of left/right putamen
Volume of left/right putamen extracted from continuous shape model
Key Investigators
Regina EY Kim, James Fishbaugh, Hans Johnson
Project Description
Objective
- Share development code
- Test on a few longidutidal data set
- Identify any immediate improvement requirement
- Identify long-term improvement requirement
- Make sure the implementation is applicable on large-scale dataset.
- See differences of Shape analysis between current and old version of segmentation
- Estimate time efficiency
- Estimate what is improved
- Identify 6 month goals/plans for Shape Analysis Project
Approach, Plan
- Sharing code: github
- Testing: 8 subjects with longitudinal data has been identified.
- Sampled from control(2), low(2), medium(2), and high(2) CAP group.
- Also sampled from 6 different sites
Progress
- Deformetrica built locally with VTK5.
- Shape modeling looks good with improved labeling approach
- Code Sharing Plan
- Source code sharing on a shared point for effective collaboration
- VTK6 Compatibility (Deformetrica)
- ITK3/4 Compatibility (ShapeWork)
- Focus area in Statistical Modeling
Shape Analysis Pipeline Installation
Shape analysis pipeline requires installation of two main tools:
- Deformetrica (James Fishbaugh)
- ShapeWork (Prasanna Muralidharan)
Deformetrica (http://www.deformetrica.org) installation
- Download 'Deformatrica 2.1' from http://www.deformetrica.org/?page_id=15
- Go to "Installation Instructions" and follow the instructions
- FFT download & installation:
$ mkdir FFTW [eunyokim@wundt /Shared/sinapse/sharedopt/UtahShapeTools ] $ cd FFTW/ [eunyokim@wundt /Shared/sinapse/sharedopt/UtahShapeTools/FFTW ] $ wget http://www.fftw.org/fftw-3.3.4.tar.gz --2015-01-06 14:27:58-- http://www.fftw.org/fftw-3.3.4.tar.gz Resolving www.fftw.org... 216.119.142.145 Connecting to www.fftw.org|216.119.142.145|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3940427 (3.8M) [application/octet-stream] Saving to: 'fftw-3.3.4.tar.gz' 100%[==================================================================================================================================================>] 3,940,427 4.44MB/s in 0.8s 2015-01-06 14:27:59 (4.44 MB/s) - 'fftw-3.3.4.tar.gz' saved [3940427/3940427] $ tar -zxvf fftw-3.3.4.tar.g
$ mkdir /Shared/sinapse/sharedopt/UtahShapeTools/FFTW/bin/ $ ./fftw-3.3.4/configure --prefix /Shared/sinapse/sharedopt/UtahShapeTools/FFTW/bin/ $ make $ make install
- Build deformetrica
$ cmake -D ITK_DIR=/Shared/sinapse/sharedopt/UtahShapeTools/ITK4/build/ -D VTK_DIR=/Shared/sinapse/scratch/eunyokim/src/NamicExternal/build_Mac_201410/VTK-build/ ../app VTK 6.2 is used. CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) CUDA was not found. Deformetrica will be compiled without Cuda -- Configuring done -- Generating done -- Build files have been written to: /Shared/sinapse/sharedopt/UtahShapeTools/deformetrica-2.1/deformetrica/bin
- build
$ make ... ... Linking CXX executable sparseMatching2 Linking CXX executable sparseMatching3 [100%] [100%] Built target sparseMatching3 Built target sparseMatching2
