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:

1. Load DICOM volume and corresponding label
2. Extract features
3. 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/