Difference between revisions of "PREDICT-HD Longitudinal Shape Analysis"
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| + | <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> | ||
| + | |||
| + | <h4> ShapeWork Installation </h4> | ||
Revision as of 00:48, 7 January 2015
Home < PREDICT-HD Longitudinal Shape Analysis
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:
- 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
