PREDICT-HD Longitudinal Shape Analysis

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Home < PREDICT-HD Longitudinal Shape Analysis

Key Investigators

Regina EY Kim, James Fishbaugh, Hans Johnson

Project Description


  • 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


  • 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:

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

Deformetrica ( installation

  1. Download 'Deformatrica 2.1' from
  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
--2015-01-06 14:27:58--
Connecting to||:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3940427 (3.8M) [application/octet-stream]
Saving to: 'fftw-3.3.4.tar.gz'

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
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

ShapeWork Installation