PREDICT-HD Longitudinal Shape Analysis

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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

Shape Analysis Pipeline Installation

Shape analysis pipeline requires installation of two main tools:

1. Deformetrica (James Fishbaugh)
2. ShapeWork (Prasanna Muralidharan)

Deformetrica (http://www.deformetrica.org) installation

1. Download 'Deformatrica 2.1' from http://www.deformetrica.org/?page_id=15
2. 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

• Install FFTW: http://www.fftw.org/fftw3_doc/Installation-on-Unix.html#Installation-on-Unix

$ 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