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>
  
 
==Key Investigators==
 
==Key Investigators==
−
Regina EY Kim
+
Regina EY Kim,
−
James Fishbaugh
+
James Fishbaugh,
 
Hans Johnson
 
Hans Johnson
  
Line 14: Line 16:
 
<h3>Objective</h3>
 
<h3>Objective</h3>
 
* Share development code
 
* Share development code
−
* Test on a few longidutidal data set
+
** 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
 
* See differences of Shape analysis between current and old version of segmentation
 
** Estimate time efficiency
 
** Estimate time efficiency
Line 22: Line 28:
 
<div style="width: 27%; float: left; padding-right: 3%;">
 
<div style="width: 27%; float: left; padding-right: 3%;">
 
<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
−
*
+
* 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
 +
 
 
</div>
 
</div>
 
<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>
 +
 +
<h3> Shape Analysis Pipeline Installation </h3>
 +
Shape analysis pipeline requires installation of two main tools:
 +
# Deformetrica (James Fishbaugh)
 +
# ShapeWork (Prasanna Muralidharan)
 +
 +
<h4> Deformetrica (http://www.deformetrica.org) installation </h4>
 +
# Download 'Deformatrica 2.1' from http://www.deformetrica.org/?page_id=15
 +
# Go to "Installation Instructions" and follow the instructions
 +
:* FFT download & installation:
 +
<pre>
 +
$ 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
 +
</pre>
 +
 +
:* Install FFTW: http://www.fftw.org/fftw3_doc/Installation-on-Unix.html#Installation-on-Unix
 +
<pre>
 +
 +
$ mkdir /Shared/sinapse/sharedopt/UtahShapeTools/FFTW/bin/
 +
$ ./fftw-3.3.4/configure --prefix /Shared/sinapse/sharedopt/UtahShapeTools/FFTW/bin/
 +
$ make
 +
$ make install
 +
</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>

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:

  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


$ 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


ShapeWork Installation

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