Moffitt 2014
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Revision as of 15:52, 22 December 2014 by Fedorov (talk | contribs) (→Notes and references for the meeting)
Home < Moffitt 2014
Logistics
SPL personnel: Andrey Fedorov, Ph.D.
Local hosts: Robert Gillies, Ph.D., Olya Grove, Ph.D.
Dates: Dec 16-17, 2014
Working meeting times:
- Tue 3-4pm
- Wed 9-10:30am
- Wed 1-3pm
Notes and references for the meeting
- Prerequisites: nightly and stable build of Slicer, Windows 64bit http://download.slicer.org
- DICOM RT conversion
- Prerequisites: SlicerRT extension, conversion script added in the last week's version of SlicerRT
- extensions are located on Windows in
C:\Users\<your_user_name>\AppData\Roaming\NA-MIC
- to enable showing hidden folders see http://windows.microsoft.com/en-us/windows/show-hidden-files#show-hidden-files=windows-7
- running Slicer python script from the command line:
Slicer.exe --no-splash --no-main-window --python-script <script> <arguments>
- to see console messages (in python interactor), run without --no-main-window flag
- make sure script name has '/', not '\', as path separator
- make sure image volume for the RTSTRUCT is in the input folder
- Lung and lesion segmentation
- FastMarching effect in Editor module
- GrowCut effect in Editor module, FastGrowCut extension
- Interfacing Matlab
- MatlabBridge extension
- Tutorial, documentation, teaching videos: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MatlabBridge
- General introduction user tutorials: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Training#General_Introduction
- Developer tutorials: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Training#Tutorials_for_software_developers
- Feature extraction: HeterogeneityCAD extension: http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD
Batch processing needed:
- Load DICOM volume and corresponding label
- Extract features
- save features in txt file
Follow-up items
- Lung and nodule segmentation and feature extraction screencast: http://youtu.be/koHKAJWGNhU
- Scripts for converting legacy PGM segmentations into Slicer-compatible format:
First, convert PGM into PNG (PGM is not recognized by Slicer image readers). Python script to do this is below. Save as a .py file, make sure python is installed, run from command line (modify the input and output directories as needed):
import Image input = '/Users/fedorov/ImageData/Moffitt/Label_conversion/MOFFITT/P2/lung/' output = '/Users/fedorov/ImageData/Moffitt/Label_conversion/MOFFITT/P2/lung-png/' for fn in range(1,163): flong = "%06i" % (fn-1) print flong Image.open(input+str(fn)+'.pgm').save(output+flong+'.png')
Raul San Jose: Airway inspector development in Slicer: http://lmi.bwh.harvard.edu/~rjosest/