Moffitt 2014

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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

  • 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
 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

Batch processing needed:

  1. Load DICOM volume and corresponding label
  2. Extract features
  3. save features in txt file

Follow-up items

  • 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/