View source for 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/