Moffitt 2014 - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:07:37Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2015-02-13T17:52:57Z

2015-02-13T17:44:05Z

2015-02-13T17:42:47Z

2014-12-26T19:16:00Z

2014-12-22T16:59:27Z

Follow-up items

2014-12-22T16:59:07Z

Follow-up items

2014-12-22T15:59:24Z

Follow-up items

2014-12-22T15:52:05Z

Notes and references for the meeting

2014-12-22T15:39:36Z

@@ Line 40: / Line 40: @@
 * Interfacing Matlab
 ** MatlabBridge extension
-** Tutorial, documentation, teaching videos: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MatlabBridge
+** Tutorial, documentation, teaching videos: https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge
 * General introduction user tutorials: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Training#General_Introduction

@@ Line 16: / Line 16: @@
 [[File:Moffitt-Slicer-Workshop-2014-pic3.jpg|350px]]
 [[File:Moffitt-Slicer-Workshop-2014-pic4.jpg|350px]]
 ==Notes and references for the meeting==

@@ Line 13: / Line 13: @@
 [[File:Moffitt-Slicer-Workshop-2014-pic1.jpg|350px]]
 [[File:Moffitt-Slicer-Workshop-2014-pic2.jpg|350px]]
 [[File:Moffitt-Slicer-Workshop-2014-pic3.jpg|350px]]
 ==Notes and references for the meeting==

@@ Line 10: / Line 10: @@
 * Wed 9-10:30am
 * Wed 1-3pm
 ==Notes and references for the meeting==

← Older revision		Revision as of 19:16, 26 December 2014
Line 158:		Line 158:

	Raul San Jose: Airway inspector development in Slicer: http://lmi.bwh.harvard.edu/~rjosest/		Raul San Jose: Airway inspector development in Slicer: http://lmi.bwh.harvard.edu/~rjosest/
		+
		+	==Slicer bugs identified during the visit==
		+	* LabelStatistics does not work occasionally. Not always reproducible. Workaround suggested: Install IASEM extension, use "Label Object Statistics" module instead.
		+	* Volume rendering of a segmented label volume is not automatically updated when editing is done: reproducible, bug reported: http://www.na-mic.org/Bug/view.php?id=3928
		+	* It seems that the image slice rendered in the 3d viewer does not go through the middle of the slice, at least when examined with slice segmentation volume rendered. May be related to existing issue: http://www.na-mic.org/Bug/view.php?id=3886
		+	*

@@ Line 50: / Line 50: @@
 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
+<pre>
-  input = '/Users/fedorov/ImageData/Moffitt/Label_conversion/MOFFITT/P2/lung/'
+import Image
-  output = '/Users/fedorov/ImageData/Moffitt/Label_conversion/MOFFITT/P2/lung-png/'
+input = '/Users/fedorov/ImageData/Moffitt/Label_conversion/MOFFITT/P2/lung/'
-  for fn in range(len(input)):
+output = '/Users/fedorov/ImageData/Moffitt/Label_conversion/MOFFITT/P2/lung-png/'
-    flong = "%06i" % (fn)
+for fn in range(len(input)):
-    print flong
+  flong = "%06i" % (fn)
-    Image.open(input+str(fn)+'.pgm').save(output+flong+'.png')
+  print flong
 Once converted to PNG, run the following script to convert the label slices into 3d format:

@@ Line 36: / Line 36: @@
 * 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:
@@ Line 43: / Line 41: @@
 # Extract features
 # save features in txt file
 Raul San Jose: Airway inspector development in Slicer: http://lmi.bwh.harvard.edu/~rjosest/