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Revision 17135 - Directory Listing
Modified Tue Aug 8 17:21:54 2017 UTC (2 months, 1 week ago) by msmolens
COMP: Fix inconsistent-missing-override warnings

This commit fixes warnings like the following:

    Slicer-0-build/EMSegment/MRML/vtkMRMLEMSNode.h:27:8: warning: 'PrintSelf' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
      void PrintSelf(ostream& os, vtkIndent indent);
           ^
    Slicer-0/Libs/MRML/Core/vtkMRMLNode.h:144:8: note: overridden virtual function is here
      void PrintSelf(ostream& os, vtkIndent indent) VTK_OVERRIDE;
           ^

From: Hina Shah <hina.shah@kitware.com>



Revision 17131 - Directory Listing
Modified Thu Jun 29 17:29:37 2017 UTC (3 months, 3 weeks ago) by msmolens
ENH: Call InitializeObjectBase() in New() methods

In VTK8 it's necessary for New() methods to call InitializeObjectBase() on the
new object for proper tracking with vtkDebugLeaks. The standard macros
(vtkStandardNewMacro, vtkObjectFactoryNewMacro) handle this. For those classes
that don't use the macros, add calls to InitializeObjectBase().

Continue to support earlier versions of VTK by wrapping calls to
InitializeObjectBase() in checks for the preprocessor define
VTK_HAS_INITIALIZE_OBJECT_BASE.

It's possible that many of these implementations could be simplified by using
the standard macros.

See also:
- https://github.com/Kitware/VTK/commit/e5c793dbdf87e838bb2b60c6a5905ced0e5548f9
- http://public.kitware.com/pipermail/vtk-developers/2016-September/034332.html


Revision 17104 - Directory Listing
Modified Fri Jun 5 13:21:15 2015 UTC (2 years, 4 months ago) by lassoan
BUG: Fixed  EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small test

Fixes error

itk::ImageFileWriterException (00000000002C51D0)
Location: "unknown" 
File: c:\d\n\slicer-1-build\itkv4\modules\io\imagebase\include\itkImageFileWriter.hxx
Line: 151
Description:  Could not create IO object for writing file C:/Users/kitware/AppData/Local/Temp/TempWriteEMS20056a03544_vtkMRMLScalarVolumeNode5/EMS20056a03544_vtkMRMLScalarVolumeNode5.h5
  Tried to create one of the following:
    NiftiImageIO
    NrrdImageIO
    GiplImageIO
    JPEGImageIO
    GDCMImageIO
    BMPImageIO
    LSMImageIO
    PNGImageIO
    TIFFImageIO
    VTKImageIO
    StimulateImageIO
    BioRadImageIO
    MetaImageIO
    MRCImageIO
    MGHImageIO
    MRMLIDImageIO

Revision 17098 - Directory Listing
Modified Sat Apr 25 21:31:35 2015 UTC (2 years, 5 months ago) by pohl
BUG: took out class 10 as the structure shown inside the probability atlas was very thin and so produce problems during testing - auto-sample failed

Revision 17096 - Directory Listing
Modified Wed Apr 8 02:15:31 2015 UTC (2 years, 6 months ago) by pohl
PERF: Made slow mode of CMTK registration more accurate

Revision 17093 - Directory Listing
Modified Fri Jan 9 17:17:37 2015 UTC (2 years, 9 months ago) by jcfr
BUG: Remove invalid BRAINSFit argument

This commit removes deprecated (and unused for a long time) command line options
from the most recent version of BRAINSTools. These command line options have
been NO-OP operations for a long time. They have been removed in the version
of BRAINSTools now used in Slicer r23872.

Thanks to "Hans Johnson <hans-johnson@uiowa.edu>" for providing the patch.

Revision 17089 - Directory Listing
Modified Mon Oct 20 23:22:11 2014 UTC (3 years ago) by pohl
STYLE: change BRAINSFIT setting to accomodate new version

Revision 17087 - Directory Listing
Modified Mon Oct 13 22:52:16 2014 UTC (3 years ago) by pohl
BUG: tcl file was not updated to VTK6

Revision 17083 - Directory Listing
Modified Wed Sep 3 17:40:47 2014 UTC (3 years, 1 month ago) by pohl
BUG: disabled calcDFVolumeNode as it calls a BRAINS function that does not work

Revision 17082 - Directory Listing
Modified Mon Sep 1 21:47:19 2014 UTC (3 years, 1 month ago) by pohl
BUG: Tests failed bc BRAINS non-rigid registration took too long - set --costFunctionConvergenceFactor to 5e+13 for test case

Revision 17077 - Directory Listing
Modified Sat Aug 30 00:50:26 2014 UTC (3 years, 1 month ago) by pohl
BUG: Integrated BRAINSTransformConvert as original cmd did not work with BRAINS anymore

Revision 17074 - Directory Listing
Modified Tue Jul 29 23:07:19 2014 UTC (3 years, 2 months ago) by pohl
BUG: BRAINS can only now read in h5 files

Revision 17069 - Directory Listing
Modified Thu Jul 10 03:47:31 2014 UTC (3 years, 3 months ago) by pohl
BUG: Extesions did not look in right directory - in addition CMTK could pass even if CMTK was not installed as EMSegmenter automatically switches to Brains

Revision 17067 - Directory Listing
Modified Tue Jul 8 16:36:23 2014 UTC (3 years, 3 months ago) by pohl
BUG: depreciated flag of BRAINS was changed

Revision 17063 - Directory Listing
Modified Mon Jun 23 17:53:31 2014 UTC (3 years, 3 months ago) by pohl
BUG: Input to vtkImageCast was not correctly set up for VTK6

Revision 17060 - Directory Listing
Modified Thu Jun 19 20:11:06 2014 UTC (3 years, 4 months ago) by pohl
BUG: Fixed bug with respect to Image inhomogeneity; included vtkImageLabelPropagation in SlicerCommonInterFaceTest1 so it would fail as this is also the reason for EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small failing

Revision 17054 - Directory Listing
Modified Fri Jun 13 02:15:34 2014 UTC (3 years, 4 months ago) by pohl
BUG: vtkSlicerCommonInterface did not define the right plugin path to plugins when EMSEgmenter was run by installed package

Revision 17053 - Directory Listing
Modified Wed Jun 11 21:41:53 2014 UTC (3 years, 4 months ago) by pohl
BUG: N4ITK changes the image range which can cause problems for images of scalar type short if they fall outside the range

Revision 17048 - Directory Listing
Modified Tue May 13 03:41:06 2014 UTC (3 years, 5 months ago) by jcfr
COMP: Simplify MRML Scene API removing "Edited()" method. Fixes #3472

Revision 17047 - Directory Listing
Modified Thu May 8 03:35:59 2014 UTC (3 years, 5 months ago) by jcfr
COMP: Fix unused variable and typdef warnings

Revision 17045 - Directory Listing
Modified Thu May 1 19:44:32 2014 UTC (3 years, 5 months ago) by finetjul
ENH: Add VTK 6 support

Revision 17042 - Directory Listing
Modified Wed Dec 4 19:51:53 2013 UTC (3 years, 10 months ago) by jcfr
COMP: Create Slicer4-EMSegment branch for current development.

Following discussion with Kilian Pohl, we agreed on creating
a dedicated branch to support the update of the module so that
it build and run against Slicer4.

It means that code pushed on [1] is expected for maintainance
of the EMSegment so that it build and run against Slicer3.

On the other hand, code pushed on [2] is non expected to be
backward compatible with Slicer3 and is done to ensure that
EMSegment build and run against Slicer4.

[1] http://svn.slicer.org/Slicer3/trunk/Modules/EMSegment
[2] http://svn.slicer.org/Slicer3/branches/Slicer4-EMSegment


For reference, the following command was used:

svn copy http://svn.slicer.org/Slicer3/trunk/Modules/EMSegment \
  http://svn.slicer.org/Slicer3/branches/Slicer4-EMSegment


Revision 17039 - Directory Listing
Modified Thu Oct 17 19:28:21 2013 UTC (4 years ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Temp Directories were not deleted at the end of the command line 

Revision 17037 - Directory Listing
Modified Thu Sep 19 19:39:33 2013 UTC (4 years, 1 month ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: a) To run EMSegmenter with tools not part of the Slicer Extension one can now only has to put them in the ~/.config/EMSegmentCustom/<Program Name> e.g. if one wants to run CMTK in Slicer4 just copy or link the bin directory of CMTK to ~/.config/EMSegmentCustom/CMTK4Slicer b) Created Testscripts for CMTK which are turned off by default c) turned off flag to run extended DefaultNode Testing

Revision 17028 - Directory Listing
Modified Tue Jul 9 03:35:07 2013 UTC (4 years, 3 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: --inputimage and --outputimage are absolute flags of N4ITKBiasFieldCorrection

Revision 17026 - Directory Listing
Modified Mon Apr 29 23:27:14 2013 UTC (4 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Skull stripping in test mode did not work

Revision 17023 - Directory Listing
Modified Fri Mar 15 03:46:17 2013 UTC (4 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: not all of CSF was part of the sub atlas

Revision 17020 - Directory Listing
Modified Fri Feb 1 23:45:44 2013 UTC (4 years, 8 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: 2 channel segmentation

Revision 17019 - Directory Listing
Modified Thu Jan 31 21:54:32 2013 UTC (4 years, 8 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: T2 image was missing

Revision 17014 - Directory Listing
Modified Tue Aug 28 20:22:14 2012 UTC (5 years, 1 month ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: LUT associated with label map were outdated causing regions to disappear when showing in visualizer

Revision 17013 - Directory Listing
Modified Mon Aug 27 16:25:50 2012 UTC (5 years, 1 month ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Slicer crashed if the name of the EMS Template node did not match the mrml file name

Revision 17011 - Directory Listing
Modified Tue Aug 7 04:25:08 2012 UTC (5 years, 2 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: EMSegCL_Task_MRIHumanBrainExp_BRAINS_small failed in Slicer 4 bc the atlas volumes were read in centered - also speed up the test

Revision 17008 - Directory Listing
Modified Sat Aug 4 00:42:32 2012 UTC (5 years, 2 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: REmoved some additional output

Revision 17007 - Directory Listing
Modified Sat Aug 4 00:34:25 2012 UTC (5 years, 2 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Removed transform node to quickly which caused the emsegmenter not to work correctly 

Revision 17003 - Directory Listing
Modified Mon Jul 30 06:00:49 2012 UTC (5 years, 2 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: #1622 remove intermediate files  

Revision 16999 - Directory Listing
Modified Thu Jul 12 23:39:50 2012 UTC (5 years, 3 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: 2050: Temporary files are removed at the end of running the comand line 

Revision 16978 - Directory Listing
Modified Thu Apr 5 07:37:28 2012 UTC (5 years, 6 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: N4 did not work correctly with multiple input channels

Revision 16974 - Directory Listing
Modified Thu Mar 15 22:50:52 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: ColorNode was not correctly defined for the task

Revision 16973 - Directory Listing
Modified Sun Mar 11 23:48:59 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Due to name changes tcl names and tests have to be changed too

Revision 16972 - Directory Listing
Modified Sun Mar 11 23:10:58 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Want to take this task out of standard list

Revision 16971 - Directory Listing
Modified Sun Mar 11 22:59:32 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Sorry for the confusion - this way it is not listed but good for testing

Revision 16970 - Directory Listing
Modified Sun Mar 11 22:58:02 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Sorry for the confusion - this way it is not listed but good for testing

Revision 16969 - Directory Listing
Modified Sun Mar 11 22:57:51 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Sorry for the confusion - this way it is not listed but good for testing

Revision 16968 - Directory Listing
Modified Sun Mar 11 22:55:42 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Sorry for the confusion - this way it is not listed but good for testing

Revision 16967 - Directory Listing
Modified Sun Mar 11 22:50:13 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: So it does not show up in the emsegmenter task list

Revision 16966 - Directory Listing
Modified Sun Mar 11 20:38:06 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: So it does not show up anymore in the user interface

Revision 16965 - Directory Listing
Modified Sun Mar 11 15:48:59 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Clean up Task list so that only robust tasks are shown

Revision 16964 - Directory Listing
Modified Sun Mar 11 15:02:50 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Not stable enough to be used yet

Revision 16959 - Directory Listing
Modified Tue Mar 6 07:31:19 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Added more debug information

Revision 16958 - Directory Listing
Modified Tue Mar 6 06:58:42 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: When directory is empty then script abroptly ended at this point 

Revision 16956 - Directory Listing
Modified Tue Feb 28 20:21:11 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: by sourcing tcl files in quotation marks and defining those in vtkEMSegmentLogic the test in Slicer 4 passed and in Slicer 3 failed - now moved to vtkSlicerCommonInterface - so that we can make them version dependent - Test-Atlas-Cluster failed with the new convention so I returned it to the old since it is only used currently in Slicer3 

Revision 16955 - Directory Listing
Modified Tue Feb 28 02:28:44 2012 UTC (5 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Functions were not called correctly when space was part of path name 

Revision 16938 - Directory Listing
Modified Fri Feb 3 10:12:52 2012 UTC (5 years, 8 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Mask has changed its name in Slicer 4

Revision 16937 - Directory Listing
Modified Fri Feb 3 09:15:07 2012 UTC (5 years, 8 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: fixed parameterization of BRAINSDemons so that EMSegCL_Task_MRIHumanBrainExp_BRAINS_small does not fail anymore

Revision 16933 - Directory Listing
Modified Sun Jan 15 07:44:01 2012 UTC (5 years, 9 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: When IntermediateDir was specified not all intermediate results got written in the directiory

Revision 16916 - Directory Listing
Modified Thu Nov 17 02:05:19 2011 UTC (5 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Intra Registration did not work anymore

Revision 16909 - Directory Listing
Modified Sun Nov 6 16:37:25 2011 UTC (5 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Related to r 1526 - EMSegmenter now works

Revision 16908 - Directory Listing
Modified Fri Nov 4 20:59:35 2011 UTC (5 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Partial fix to #1524

Revision 16895 - Directory Listing
Modified Wed Oct 26 02:22:31 2011 UTC (5 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Error Appeared when Disabling non-rigid for BRAINS registration 

Revision 16882 - Directory Listing
Modified Wed Oct 12 22:15:26 2011 UTC (6 years ago) by jcfr
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Fix indent

Revision 16818 - Directory Listing
Modified Sun Aug 14 23:20:48 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Use plastimatch's new --output_type to specify the pixeltype

Revision 16817 - Directory Listing
Modified Sun Aug 14 00:32:28 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Use Slicer's Cast module instead of ANTS's ConvertImagePixelType

Revision 16816 - Directory Listing
Modified Sat Aug 13 22:02:17 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: nrrd conversion fixed upstream http://itk.org/gitweb?p=ITK.git;a=commit;h=5e4210fc

Revision 16810 - Directory Listing
Modified Wed Aug 10 21:18:37 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Use the new tcl filename for BRAINS

Revision 16802 - Directory Listing
Modified Tue Aug 9 18:29:06 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Refactor registration packages

Revision 16799 - Directory Listing
Modified Fri Aug 5 15:50:40 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Change test parameter

Revision 16798 - Directory Listing
Modified Fri Aug 5 15:49:51 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: set pixeltype for plastimatch

Revision 16797 - Directory Listing
Modified Thu Aug 4 17:25:20 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: always source BRAINS functions

Revision 16796 - Directory Listing
Modified Thu Aug 4 17:06:45 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Move BRAINS code into separate file

Revision 16795 - Directory Listing
Modified Thu Aug 4 16:51:00 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Move CMTK code into separate file

Revision 16794 - Directory Listing
Modified Thu Aug 4 16:46:03 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Move DEMONS code into separate file

Revision 16793 - Directory Listing
Modified Thu Aug 4 16:41:27 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Move CMTK code into separate file

Revision 16792 - Directory Listing
Modified Thu Aug 4 16:34:51 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Move plastimatch code into separate file

Revision 16769 - Directory Listing
Modified Tue Jul 26 17:11:59 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: remove colorNodeRef="vtkMRMLFreeSurferColorNodeLabels" because of Error in Slicer4

Revision 16768 - Directory Listing
Modified Tue Jul 26 16:00:54 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Fix path to test data

Revision 16765 - Directory Listing
Modified Mon Jul 25 20:32:25 2011 UTC (6 years, 2 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added DEMONS registration support

Revision 16762 - Directory Listing
Modified Fri Jul 22 19:22:54 2011 UTC (6 years, 3 months ago) by haehn
Original Path: trunk/Modules/EMSegment/Tasks
ENH: EMSegment: Fixed tests for Slicer4.

 * Several changes to the .tcl files to access functionality in a general way for Slicer3 and Slicer4.
 * Several changes to the Qt Widgets to synchronize with the MRML scene properly in Slicer4.
 * Removed dependenices to the Slicer3 GUI.




Revision 16758 - Directory Listing
Modified Fri Jul 22 01:34:14 2011 UTC (6 years, 3 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Fixed plastimatch registration call

Revision 16734 - Directory Listing
Modified Sat Jul 9 04:00:27 2011 UTC (6 years, 3 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Add basic plastimatch support (currently without resampling)

Revision 16715 - Directory Listing
Modified Wed Jun 29 17:38:03 2011 UTC (6 years, 3 months ago) by haehn
Original Path: trunk/Modules/EMSegment/Tasks
ENH: EMSegment: Un-tied the tcl files from the GUI.

 * This was necessary for the Slicer4 port.
 * To untie from the GUI, the tcl interface had to be changed like this:

   * in simple and advanced mode, a pointer to the EMSegmentLogic has to be passed to:
     proc ShowUserInterface { {LOGIC ""} }

   * this will call the [InitVariables $LOGIC] function with the logic as an argument

   * in InitVariables, the Logic will be queried for the SlicerCommonInterface which then
     provides the following functions to access parts of the GUI:

     // Slicer3
     vtkEMSegmentKWDynamicFrame* GetSimpleDynamicFrame();
     vtkEMSegmentKWDynamicFrame* GetAdvancedDynamicFrame();

     // Slicer4
     vtkSlicerCommonInterface* GetSimpleDynamicFrame();
     vtkSlicerCommonInterface* GetAdvancedDynamicFrame();

   * this commit only includes the Slicer3 functionality

   * vtkSlicerCommonInterface holds also the same methods as vtkEMSegmentKWDynamicFrame so that the tcl
     tasks can access the convenience methods to create GUI elements in the same way in Slicer3 and Slicer4

 * Changing the tcl interface included changes to GenericTask.tcl, all other tcl-Task files and the Template.tcl

 * The EMSegmentGUI and the Tests pass



Revision 16702 - Directory Listing
Modified Sat Jun 18 23:00:13 2011 UTC (6 years, 4 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Assign intensity label 0 to background class

Revision 16700 - Directory Listing
Modified Fri Jun 17 02:37:39 2011 UTC (6 years, 4 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added lesion specific preprocessing file

Revision 16699 - Directory Listing
Modified Fri Jun 17 02:19:14 2011 UTC (6 years, 4 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Remove air and skull classes

Revision 16698 - Directory Listing
Modified Fri Jun 17 01:01:07 2011 UTC (6 years, 4 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Rename BiasCorrectionType

Revision 16691 - Directory Listing
Modified Wed Jun 15 19:02:21 2011 UTC (6 years, 4 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Add Lesion segmentation task

Revision 16678 - Directory Listing
Modified Tue Jun 7 19:34:19 2011 UTC (6 years, 4 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Create temporary files using C++ , command line tools are not available on all platforms

Revision 16666 - Directory Listing
Modified Thu Jun 2 17:23:41 2011 UTC (6 years, 4 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Use POSIX functions to generate temporary filenames and directories instead of commandline tools

Revision 16660 - Directory Listing
Modified Fri May 27 22:17:23 2011 UTC (6 years, 4 months ago) by haehn
Original Path: trunk/Modules/EMSegment/Tasks
ENH: EMSegment4: Tcl Code Execution now works.

 - added new test for the vtkSlicerCommonInterface to check if Tcl code can run properly on Slicer3 and Slicer4
 - Untied the GUI from GenericTask.tcl by replacing calls to GetTemporaryDirectory and GetPluginsDir to equivalent calls in the EMLogic
 - added methodhandler to handle tcl through python code in Slicer4 properly



Revision 16633 - Directory Listing
Modified Thu May 19 15:09:13 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Changed CSF label to 18

Revision 16628 - Directory Listing
Modified Wed May 18 05:44:18 2011 UTC (6 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Alex wanted different labels

Revision 16623 - Directory Listing
Modified Mon May 16 18:02:58 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Changed signatur of PerformIntensityCorrection

Revision 16620 - Directory Listing
Modified Fri May 13 21:36:15 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Split AtlasCreator into 2 functions (AtlasCreator and UpdateAtlas)

Revision 16609 - Directory Listing
Modified Thu May 12 13:02:09 2011 UTC (6 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Should fix bug with respect to orientation of atlas

Revision 16608 - Directory Listing
Modified Wed May 11 21:38:13 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: set centerImage="1"

Revision 16607 - Directory Listing
Modified Wed May 11 21:36:19 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Add scheduler command, SetIgnoreTemplateSegmentation 1

Revision 16606 - Directory Listing
Modified Wed May 11 18:42:00 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Moved output to the right location

Revision 16598 - Directory Listing
Modified Tue May 10 22:04:50 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added a text entry for the segmentation labels

Revision 16594 - Directory Listing
Modified Tue May 10 14:36:39 2011 UTC (6 years, 5 months ago) by haehn
Original Path: trunk/Modules/EMSegment/Tasks
ENH: EMSegment:

 - add support to call the AtlasCreator when using the EMSegment CommandlineTool which only provides a "lite" Slicer environment without the modules and the GUI
 - this was done by adding Python support to the vtkSlicerCommonInterface which then gets used by the EMSegment CommandlineTool to access the Python based AtlasCreator logic
 - since Slicer3 uses Python through Tcl we had to perform some magic :)



Revision 16584 - Directory Listing
Modified Fri May 6 19:00:24 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added debugging output

Revision 16579 - Directory Listing
Modified Fri May 6 15:51:38 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: get prior from leaf, not from prior itself

Revision 16577 - Directory Listing
Modified Thu May 5 21:30:07 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added debug output

Revision 16576 - Directory Listing
Modified Thu May 5 20:50:37 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: set ERROR_NODE_VTKID 0

Revision 16575 - Directory Listing
Modified Thu May 5 20:25:28 2011 UTC (6 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Hopefully fixed bug with atlas creator

Revision 16574 - Directory Listing
Modified Thu May 5 19:02:46 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: removed wrapper function CreateVolumeNode

Revision 16573 - Directory Listing
Modified Thu May 5 18:33:17 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Fix wrapper around  CreateVolumeScalarNode

Revision 16571 - Directory Listing
Modified Thu May 5 16:32:32 2011 UTC (6 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Move tcl code into MRML Manager to make it cleaner

Revision 16569 - Directory Listing
Modified Thu May 5 13:12:04 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Specify width for text entry

Revision 16566 - Directory Listing
Modified Wed May 4 21:29:17 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Changed a few comments

Revision 16565 - Directory Listing
Modified Wed May 4 21:27:32 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Restructured  proc AtlasCreator

Revision 16563 - Directory Listing
Modified Wed May 4 20:44:27 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Add function proc CreateNewVolumeNodeAndAddToScene { name }

Revision 16562 - Directory Listing
Modified Tue May 3 22:13:26 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Changed indentation

Revision 16555 - Directory Listing
Modified Tue May 3 19:24:38 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG:Replaced | by :

Revision 16554 - Directory Listing
Modified Tue May 3 19:23:18 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Changed label from 4 to 220 - other wise label 4 and 25 are too similar

Revision 16545 - Directory Listing
Modified Mon May 2 17:15:03 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Turn on registration

Revision 16543 - Directory Listing
Modified Mon May 2 16:19:16 2011 UTC (6 years, 5 months ago) by haehn
Original Path: trunk/Modules/EMSegment/Tasks
ENH: EMSegment:

 - the old KWLogic is now integrated in the real EMSegmentLogic
 - modified the GUI and the tcl files accordingly
 - the EMSegmentLogic uses the TclConnector functionality to run Tcl code or to interact with the Tcl interpreter
 - other code dependent on KWWidgets was moved to the Slicer3Helper
 - finally deleted the KWLogic class



Revision 16542 - Directory Listing
Modified Mon May 2 15:14:55 2011 UTC (6 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Path was not relative 

Revision 16536 - Directory Listing
Modified Sun May 1 03:44:12 2011 UTC (6 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Creates a segmentation of two hemispheres - other than that same as MRI-Human-Brain

Revision 16535 - Directory Listing
Modified Fri Apr 29 20:23:13 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Use accurate parameter

Revision 16531 - Directory Listing
Modified Thu Apr 28 22:22:35 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Change labelmap to vtkMRMLFreeSurferColorNodeLabels

Revision 16527 - Directory Listing
Modified Thu Apr 28 18:56:18 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Use BRAINSTools in accurate mode per default

Revision 16518 - Directory Listing
Modified Thu Apr 28 03:53:26 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Use a leading ':' and change ';' to ':' because of midas bug

Revision 16514 - Directory Listing
Modified Wed Apr 27 23:46:52 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: replace | by ;

Revision 16512 - Directory Listing
Modified Wed Apr 27 22:28:20 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Replace | by ;

Revision 16510 - Directory Listing
Modified Wed Apr 27 22:25:46 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Replace | by ;

Revision 16504 - Directory Listing
Modified Wed Apr 27 19:45:36 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: match brackets in comments

Revision 16499 - Directory Listing
Modified Tue Apr 26 21:28:00 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Call BRAINSFit only once

Revision 16496 - Directory Listing
Modified Tue Apr 26 19:50:42 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Fixed tmpfile issue 'removing old version of file...'

Revision 16490 - Directory Listing
Modified Tue Apr 26 03:03:26 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Removed redundant code and added the function: proc CMTKGetPixelTypeFromVolumeNode { volumeNode }

Revision 16486 - Directory Listing
Modified Mon Apr 25 03:00:51 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: More cleanup

Revision 16485 - Directory Listing
Modified Mon Apr 25 02:30:39 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: the variable outputAtlasNode didn't exist, use alignedAtlasNode instead

Revision 16484 - Directory Listing
Modified Sun Apr 24 21:38:39 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Create function BRAINSGetPixelTypeFromVolumeNode , Use improved BRAINSFit parameter

Revision 16483 - Directory Listing
Modified Sun Apr 24 12:57:00 2011 UTC (6 years, 5 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Use BRAINSFit option --constMetric MMI

Revision 16479 - Directory Listing
Modified Fri Apr 22 12:42:46 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: use --costMetric MM

Revision 16474 - Directory Listing
Modified Thu Apr 21 20:37:46 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Write each BRAINSFit option in one line to make it more readable

Revision 16471 - Directory Listing
Modified Thu Apr 21 16:02:15 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: print correct flagname

Revision 16470 - Directory Listing
Modified Thu Apr 21 15:34:50 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Updated indentation

Revision 16469 - Directory Listing
Modified Thu Apr 21 15:33:40 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Merge with my changes

Revision 16468 - Directory Listing
Modified Thu Apr 21 08:17:16 2011 UTC (6 years, 6 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Fixed bug with storage node and ct hand bone segmentation

Revision 16467 - Directory Listing
Modified Thu Apr 21 02:02:31 2011 UTC (6 years, 6 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added function for creating background atlas

Revision 16466 - Directory Listing
Modified Wed Apr 20 22:46:26 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Removed inhomogeneityCorrection

Revision 16445 - Directory Listing
Modified Tue Apr 19 17:53:33 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Changed finger names

Revision 16444 - Directory Listing
Modified Tue Apr 19 17:53:07 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Changed finger names

Revision 16434 - Directory Listing
Modified Mon Apr 18 19:27:07 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: remove label(class) 3 and 7

Revision 16433 - Directory Listing
Modified Mon Apr 18 17:50:08 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: remove EMSWorkingData

Revision 16432 - Directory Listing
Modified Mon Apr 18 17:41:42 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Set standard preprocessing: aff.reg.=acc def.reg.=fast reg.=on inh.cor.=on

Revision 16431 - Directory Listing
Modified Mon Apr 18 17:25:54 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Removed a redundant tree node

Revision 16430 - Directory Listing
Modified Mon Apr 18 17:09:44 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Update path to atlas file 

Revision 16428 - Directory Listing
Modified Mon Apr 18 04:38:51 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Use non trivial LogCovarianceCorrection

Revision 16427 - Directory Listing
Modified Mon Apr 18 04:20:31 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Use non trivial LogCovarianceCorrection

Revision 16422 - Directory Listing
Modified Fri Apr 15 20:59:19 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Simplified anatomical tree

Revision 16390 - Directory Listing
Modified Wed Apr 13 16:13:20 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added a new task 'Human-Eye' 

Revision 16355 - Directory Listing
Modified Fri Apr 8 04:59:32 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: reduce numberOfIterations in test mode

Revision 16354 - Directory Listing
Modified Fri Apr 8 04:32:47 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: CMTK can now handle uint volumes

Revision 16347 - Directory Listing
Modified Thu Apr 7 21:46:28 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG:
clarified variable name (transformation_Node_or_FileName)
fixed bug in atlas creator function
normalize to 100 per default if set to ON
fixed bug in deformation field generation if affine registration = ON and deformable registration = OFF
updated indentation



Revision 16342 - Directory Listing
Modified Thu Apr 7 15:16:44 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Restore LogMean values

Revision 16331 - Directory Listing
Modified Wed Apr 6 16:12:17 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: don't use slicers source dir to access atlas files

Revision 16330 - Directory Listing
Modified Wed Apr 6 13:31:56 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Set all default Mean/Log values to 0

Revision 16329 - Directory Listing
Modified Wed Apr 6 02:57:06 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Remove reference to Slicer3_2010_Brain_Labels.txt - use now GenericAnatomyColors.txt

Revision 16327 - Directory Listing
Modified Tue Apr 5 23:14:31 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Update mrml files

Revision 16320 - Directory Listing
Modified Tue Apr 5 14:23:42 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Update CT-Hand-Bone task because of API change in EMSegment MRML manager

Revision 16309 - Directory Listing
Modified Mon Apr 4 02:51:52 2011 UTC (6 years, 6 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Seperated KW from rest to simplify transition to Slicer4

Revision 16300 - Directory Listing
Modified Sun Apr 3 05:49:07 2011 UTC (6 years, 6 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Just added a comment 

Revision 16299 - Directory Listing
Modified Sun Apr 3 05:37:11 2011 UTC (6 years, 6 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Full Parcellation Works now with CMTK

Revision 16298 - Directory Listing
Modified Sat Apr 2 23:03:12 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Update test atlas creator task

Revision 16296 - Directory Listing
Modified Sat Apr 2 18:11:19 2011 UTC (6 years, 6 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: I cleaned up code to ease transition to Slicer4

Revision 16284 - Directory Listing
Modified Fri Apr 1 22:22:14 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Removed unused key : 'Key atlas_registration_image NodeID vtkMRMLScalarVolumeNode19' 

Revision 16283 - Directory Listing
Modified Fri Apr 1 20:31:45 2011 UTC (6 years, 6 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Results of Atlas Creator were not correctly read in

Revision 16273 - Directory Listing
Modified Thu Mar 31 15:33:55 2011 UTC (6 years, 6 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Simplified code

Revision 16270 - Directory Listing
Modified Wed Mar 30 19:10:29 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added label description

Revision 16256 - Directory Listing
Modified Sat Mar 26 01:05:08 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Update Test-Atlas-Cluster task

Revision 16254 - Directory Listing
Modified Fri Mar 25 03:19:01 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Write AC results back into mrml scene

Revision 16253 - Directory Listing
Modified Fri Mar 25 03:18:33 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Write AC results back into mrml scene

Revision 16243 - Directory Listing
Modified Wed Mar 23 19:22:03 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: set default values for the Atlas Creator 

Revision 16239 - Directory Listing
Modified Wed Mar 23 16:42:47 2011 UTC (6 years, 6 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Add options to AtlasCreator function

Revision 16221 - Directory Listing
Modified Fri Mar 18 15:03:56 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: remove unused backup file

Revision 16220 - Directory Listing
Modified Fri Mar 18 15:00:39 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Cleanup

Revision 16219 - Directory Listing
Modified Fri Mar 18 14:59:27 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Add a prototype inpreparation to use the Atlas Creator

Revision 16218 - Directory Listing
Modified Fri Mar 18 14:57:28 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Clean up

Revision 16217 - Directory Listing
Modified Fri Mar 18 14:56:42 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Improve Skull Stripper (added switch between CMTK and BRAINS )

Revision 16216 - Directory Listing
Modified Fri Mar 18 14:53:23 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Specify SkullStripper related files here instead of in the mrml scene

Revision 16215 - Directory Listing
Modified Fri Mar 18 14:51:46 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Remove unused volumes

Revision 16201 - Directory Listing
Modified Wed Mar 16 18:03:39 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Add prototype function for the AtlasCreator

Revision 16200 - Directory Listing
Modified Wed Mar 16 00:31:19 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Update description of preprocessing checkboxes

Revision 16199 - Directory Listing
Modified Wed Mar 16 00:30:15 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Use Colormap="vtkMRMLColorTableNodeFileSlicer3_2010_Brain_Labels.txt" 

Revision 16198 - Directory Listing
Modified Tue Mar 15 19:28:17 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Adding task for skull stripped brain images

Revision 16194 - Directory Listing
Modified Tue Mar 15 14:36:07 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: (BSplineToDeformationField) Send normal output to stdout instead of stderr , Use 'eval exec ' to execute a command

Revision 16189 - Directory Listing
Modified Mon Mar 14 21:59:51 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Improve error handling for function calcDFVolumeNode

Revision 16181 - Directory Listing
Modified Mon Mar 14 18:00:54 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: CMTK's registration/warp command cannot change the scalar type of the output volume, resample the atlas in an additional step

Revision 16168 - Directory Listing
Modified Wed Mar 9 16:53:55 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: pass --fast --verbose options to each CMTK call

Revision 16121 - Directory Listing
Modified Sat Feb 26 06:25:03 2011 UTC (6 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: colormap did not exist anymore

Revision 16119 - Directory Listing
Modified Sat Feb 26 05:44:21 2011 UTC (6 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Based on Rons feedback we slightly modified the atlases

Revision 16117 - Directory Listing
Modified Sat Feb 26 05:18:24 2011 UTC (6 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Based on Rons feedback we slightly modified the atlases

Revision 16116 - Directory Listing
Modified Sat Feb 26 05:14:31 2011 UTC (6 years, 7 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Based on Rons feedback we slightly modified the atlases

Revision 16109 - Directory Listing
Modified Thu Feb 24 20:58:13 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: we have to set the backgroundLevel to get rid of the segmentation errors outside the target volume

Revision 16085 - Directory Listing
Modified Mon Feb 21 22:55:54 2011 UTC (6 years, 7 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added support for multiple scalartypes (if using CMTK)

Revision 16051 - Directory Listing
Modified Wed Feb 16 01:25:43 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: remove some warp options: --delay-refine --exact-spacing

Revision 16047 - Directory Listing
Modified Tue Feb 15 22:34:00 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: turning on the multi-resolution image pyramid

Revision 16044 - Directory Listing
Modified Tue Feb 15 17:12:25 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Replace raw .nrrd files

Revision 16037 - Directory Listing
Modified Mon Feb 14 19:46:26 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added --fast option to CMTK's warp command

Revision 16005 - Directory Listing
Modified Sat Feb 12 01:23:42 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Fixed taskname

Revision 16004 - Directory Listing
Modified Sat Feb 12 01:22:32 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added a warning message if CMTK is not installed

Revision 16002 - Directory Listing
Modified Fri Feb 11 21:42:21 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Changed parameter for fast test mode

Revision 15995 - Directory Listing
Modified Fri Feb 11 14:29:13 2011 UTC (6 years, 8 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Updated sub parcellation with label map from cca atlas v5_1

Revision 15994 - Directory Listing
Modified Fri Feb 11 14:22:46 2011 UTC (6 years, 8 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Subparcellation was not correctly performed when skipping registration - this is fixed now

Revision 15991 - Directory Listing
Modified Fri Feb 11 02:47:31 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: CMTK is now used per default

Revision 15990 - Directory Listing
Modified Fri Feb 11 02:34:41 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Simplified mrml files

Revision 15989 - Directory Listing
Modified Fri Feb 11 02:34:18 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Changed they way mktemp is called because the X's had to appear at the template end (e.g. on Fedora) 

Revision 15977 - Directory Listing
Modified Wed Feb 9 22:17:37 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added fast running tests - using CMTK and BRAINS

Revision 15970 - Directory Listing
Modified Tue Feb 8 23:26:54 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Now it is possible to choose between different registration packages

Revision 15969 - Directory Listing
Modified Tue Feb 8 23:21:51 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Now it is possible to choose between different registration packages

Revision 15965 - Directory Listing
Modified Tue Feb 8 05:48:20 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: update CMTK functionality

Revision 15964 - Directory Listing
Modified Mon Feb 7 22:55:00 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: change some backslash and quotations marks

Revision 15960 - Directory Listing
Modified Mon Feb 7 02:57:35 2011 UTC (6 years, 8 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Updated fast registration

Revision 15959 - Directory Listing
Modified Mon Feb 7 01:36:50 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Set backslash and quotation marks around variables - this is necessary because there might be white spaces in the variable names

Revision 15951 - Directory Listing
Modified Sun Feb 6 18:11:11 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: fixed bug in test EMSegCL_IntermediateResults: 'UpdateScene: error getting 0th storage node'

Revision 15942 - Directory Listing
Modified Sun Feb 6 00:41:11 2011 UTC (6 years, 8 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Simplified EMSegmenters MRML Structure in preperation for Slicer 4

Revision 15919 - Directory Listing
Modified Fri Feb 4 16:32:17 2011 UTC (6 years, 8 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Cleaned up registration Type

Revision 15915 - Directory Listing
Modified Fri Feb 4 00:02:41 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Remove old unused SlicerRigidRegister function

Revision 15910 - Directory Listing
Modified Thu Feb 3 00:17:42 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Use the same mktemp options on all platforms

Revision 15906 - Directory Listing
Modified Wed Feb 2 16:28:51 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Don't call BRAINSSkullStripper as long it is in development

Revision 15905 - Directory Listing
Modified Wed Feb 2 16:26:38 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: mktemp options differ on Linux and Darwin

Revision 15904 - Directory Listing
Modified Wed Feb 2 15:51:33 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Use mktemp -t instead of deprecated -p option

Revision 15903 - Directory Listing
Modified Wed Feb 2 01:31:52 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Refactored all tasks

Revision 15897 - Directory Listing
Modified Tue Feb 1 22:25:09 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: change signature of function fiducial_threshold , we don't use fiducials right now

Revision 15866 - Directory Listing
Modified Sun Jan 30 22:46:54 2011 UTC (6 years, 8 months ago) by pieper
Original Path: trunk/Modules/EMSegment/Tasks
COMP: fix warnings about unused variables

Revision 15803 - Directory Listing
Modified Fri Jan 21 23:38:34 2011 UTC (6 years, 8 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added new preprocessing pipeline for CT-Hand-Bone task

Revision 15785 - Directory Listing
Modified Wed Jan 19 21:12:51 2011 UTC (6 years, 9 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Don't call  PopUpWarningWindow "", GUI is not available in command line mode

Revision 15778 - Directory Listing
Modified Tue Jan 18 16:18:57 2011 UTC (6 years, 9 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: PATH was not set correctly for plugin modules under windows

Revision 15763 - Directory Listing
Modified Thu Jan 13 06:16:04 2011 UTC (6 years, 9 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Replaced micro

Revision 15749 - Directory Listing
Modified Mon Jan 10 09:10:05 2011 UTC (6 years, 9 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Include full parcellation pipeline

Revision 15694 - Directory Listing
Modified Sun Dec 26 19:39:18 2010 UTC (6 years, 9 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Update atlas data

Revision 15673 - Directory Listing
Modified Sat Dec 18 01:06:01 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added a mrml scene for the new 'CT Hand Bone' task

Revision 15656 - Directory Listing
Modified Wed Dec 15 01:08:22 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Calculate a deformation field to speed up the resampling

Revision 15649 - Directory Listing
Modified Mon Dec 13 20:53:14 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Create a deformation field to accelerate the resampling

Revision 15646 - Directory Listing
Modified Mon Dec 13 20:33:08 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Fixed Typo

Revision 15641 - Directory Listing
Modified Fri Dec 10 22:20:08 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Use N4ITKBiasFieldCorrectionCLI instead of GUI module 'N4ITK MRI Bias correction'

Revision 15640 - Directory Listing
Modified Fri Dec 10 22:09:05 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Fixed thresholding, it is important in what order to set the parameter

Revision 15638 - Directory Listing
Modified Fri Dec 10 19:22:20 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Threshold target image(s), negative values will be set to 0 so that the EMSegmenter can be used on those images.

Revision 15624 - Directory Listing
Modified Wed Dec 8 15:21:25 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Fixed bug in Resample -> PrintError

Revision 15623 - Directory Listing
Modified Wed Dec 8 15:16:00 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Applied automatic indentation

Revision 15616 - Directory Listing
Modified Mon Dec 6 20:49:26 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added wrapper function for SkullStripperCLI

Revision 15606 - Directory Listing
Modified Sat Dec 4 08:44:04 2010 UTC (6 years, 10 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: removed some bugs

Revision 15605 - Directory Listing
Modified Sat Dec 4 07:01:54 2010 UTC (6 years, 10 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Integration of subparcellation capabilties Part II

Revision 15603 - Directory Listing
Modified Fri Dec 3 20:28:20 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Moved code to GenericTask.tcl

Revision 15584 - Directory Listing
Modified Wed Nov 24 23:09:00 2010 UTC (6 years, 10 months ago) by fedorov
Original Path: trunk/Modules/EMSegment/Tasks
BUG: CGM = cortical GM


Revision 15583 - Directory Listing
Modified Wed Nov 24 22:34:38 2010 UTC (6 years, 10 months ago) by fedorov
Original Path: trunk/Modules/EMSegment/Tasks
ENH: assigned meaningful names to the segmented structures


Revision 15567 - Directory Listing
Modified Tue Nov 23 23:04:13 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Removed hardcoded path

Revision 15564 - Directory Listing
Modified Tue Nov 23 21:52:31 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added new task 'Non-Human primate'

Revision 15563 - Directory Listing
Modified Tue Nov 23 21:42:00 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added template file which can be used to create new tasks

Revision 15562 - Directory Listing
Modified Tue Nov 23 21:38:20 2010 UTC (6 years, 10 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added unbiased atlas data, Downloaded from http://www.nitrc.org/projects/vervet_atlas (VPA10-2.0.zip - 2010-07-02) 

Revision 15561 - Directory Listing
Modified Tue Nov 23 19:16:55 2010 UTC (6 years, 10 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Curtis correctly wraps now vtkMRMLFinite* so we were able to simplify the code

Revision 15529 - Directory Listing
Modified Fri Nov 19 16:40:15 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Inform the user to apply this task only to skull stripped data

Revision 15528 - Directory Listing
Modified Fri Nov 19 16:35:14 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Adding a pre-processing file for the MRI-Human-Brain-Parcellation task

Revision 15519 - Directory Listing
Modified Wed Nov 17 16:16:23 2010 UTC (6 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: parameters were not set correctly

Revision 15506 - Directory Listing
Modified Tue Nov 16 03:10:15 2010 UTC (6 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Made small changes to the file so it runs more efficiently

Revision 15502 - Directory Listing
Modified Mon Nov 15 15:17:18 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Turn on image inhomogeneity correction per default

Revision 15489 - Directory Listing
Modified Fri Nov 12 18:57:36 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added a new MRI Human Head pipeline for a finer-grained parcellation based on data provided by Padmapriya Srinivasan and Sylvain Bouix (PNL-BWH)

Revision 15474 - Directory Listing
Modified Thu Nov 11 21:00:34 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Change parameter for BRAINSFit: Increase the numberOfSamples, also increase the splineGridSize

Revision 15465 - Directory Listing
Modified Thu Nov 11 15:41:37 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Moved task specific atlas data into a subdirectory

Revision 15426 - Directory Listing
Modified Wed Nov 3 18:24:52 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Use BRAINSResampleCLI instead of the BRAINSResample GUI module

Revision 15419 - Directory Listing
Modified Wed Nov 3 15:30:24 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Use a hardcoded svn revision number if GetSvnRevision is not set

Revision 15414 - Directory Listing
Modified Wed Nov 3 02:00:06 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Take advantage of UseBRAINS variable to switch between BRAINS and CMTK

Revision 15413 - Directory Listing
Modified Wed Nov 3 01:36:55 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Add function to use CMTK's reformat

Revision 15410 - Directory Listing
Modified Tue Nov 2 21:54:26 2010 UTC (6 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: BRAINSFit now works again

Revision 15397 - Directory Listing
Modified Tue Nov 2 02:48:38 2010 UTC (6 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Addressed bug discovered by Daniel and Ron where pipeline did not work correctly with two input channels

Revision 15391 - Directory Listing
Modified Sat Oct 30 21:55:54 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added rudimentary support for CMTK registration

Revision 15379 - Directory Listing
Modified Fri Oct 29 20:23:14 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Don't perform segmentation if excecution of registration fails

Revision 15366 - Directory Listing
Modified Thu Oct 28 18:44:00 2010 UTC (6 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Do avoid downloading data from web we now store the data in repository - will hopefully  be changed for Slicer 3.6.3. release

Revision 15364 - Directory Listing
Modified Thu Oct 28 06:11:07 2010 UTC (6 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Tried to modify BRAINSFit paramters according to Hans but did not work so I changed them back again, created a function for DataIO, moved some functions from MRMLManager to Logic, adjusted the tests so that they would compile with new structure, included capabilities for propagating error messages from EMSegmenter to GUI via pop up window

Revision 15331 - Directory Listing
Modified Mon Oct 25 18:25:47 2010 UTC (6 years, 11 months ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: use .mat extension for transformation files

Revision 15307 - Directory Listing
Modified Fri Oct 22 18:22:40 2010 UTC (6 years, 11 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Remove meaningless error msg as it confuses testing 

Revision 15297 - Directory Listing
Modified Fri Oct 22 06:01:27 2010 UTC (7 years ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Made Command Line work - hasd to replace fetchmi for downloading files

Revision 15290 - Directory Listing
Modified Thu Oct 21 21:11:46 2010 UTC (7 years ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Comment-out old code which causes memory leaks

Revision 15268 - Directory Listing
Modified Thu Oct 21 08:29:15 2010 UTC (7 years ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: fixed error with selecting Preprocessing in first step and check covariance matrix 

Revision 15267 - Directory Listing
Modified Thu Oct 21 01:20:12 2010 UTC (7 years ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: PATH was not set correctly for plugin modules under windows

Revision 15265 - Directory Listing
Modified Wed Oct 20 07:25:34 2010 UTC (7 years ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Addressed all issues voiced by Daniel, corrected the import bug, and modified code to reduce unimportant error messages show up in shell 

Revision 15242 - Directory Listing
Modified Tue Oct 19 09:35:37 2010 UTC (7 years ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: small info change 

Revision 15241 - Directory Listing
Modified Tue Oct 19 09:23:33 2010 UTC (7 years ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Template Creater did not work correctly - updated mrml file to represent new structure

Revision 15240 - Directory Listing
Modified Tue Oct 19 04:03:03 2010 UTC (7 years ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Fixed bugs related to the EMSegmenter

Revision 15177 - Directory Listing
Modified Mon Oct 11 02:40:14 2010 UTC (7 years ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Cast atlas volumes to the same scalar type as the target volumes

Revision 15126 - Directory Listing
Modified Thu Sep 30 16:02:09 2010 UTC (7 years ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: Added functionality to call N4ITKBiasFieldCorrectionCLI from EMSegmentCommandLine

Revision 15123 - Directory Listing
Modified Thu Sep 30 15:04:58 2010 UTC (7 years ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Added "TCLMRI: " to each puts command

Revision 15121 - Directory Listing
Modified Thu Sep 30 14:35:07 2010 UTC (7 years ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: Added "TCL: " to each puts command

Revision 15116 - Directory Listing
Modified Wed Sep 29 20:41:55 2010 UTC (7 years ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: remove command line node after the command line is executed

Revision 15110 - Directory Listing
Modified Wed Sep 29 20:02:59 2010 UTC (7 years ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
ENH: remove command line node after the command line is executed

Revision 15102 - Directory Listing
Modified Tue Sep 28 15:52:41 2010 UTC (7 years ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: removed trailing whitespaces and applied automatic indentation

Revision 15085 - Directory Listing
Modified Fri Sep 24 23:10:12 2010 UTC (7 years ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Commit cosmetic changes based on Ron's feedback

Revision 15052 - Directory Listing
Modified Thu Sep 23 18:19:26 2010 UTC (7 years ago) by domibel
Original Path: trunk/Modules/EMSegment/Tasks
STYLE: removed trailing whitespaces and applied automatic indentation

Revision 15041 - Directory Listing
Modified Wed Sep 22 18:55:34 2010 UTC (7 years ago) by pieper
Original Path: trunk/Modules/EMSegment/Tasks
ENH: make Slicer3/trunk be a copy of Slicer-3-6 branch.  New slicer4 development has moved to http://svn.slicer.org/Slicer4/trunk.  Use the Slicer3 trunk only for slicer3 maint purposes.

See this desription for details:

http://massmail.spl.harvard.edu/public-archives/slicer-devel/2010/005338.html


Revision 15022 - Directory Listing
Modified Mon Sep 20 11:05:59 2010 UTC (7 years, 1 month ago) by pohl
Original Path: branches/Slicer-3-6/Modules/EMSegment/Tasks
BUG: addresses bug 972

Revision 15021 - Directory Listing
Modified Sat Sep 18 07:48:40 2010 UTC (7 years, 1 month ago) by pohl
Original Path: branches/Slicer-3-6/Modules/EMSegment/Tasks
BUG: Now in simple mode the gui steps are not shown anymore, I updated the help, inncluded automatic computation of training samples, and fixed the autosampling bug

Revision 14986 - Directory Listing
Modified Mon Sep 13 03:55:14 2010 UTC (7 years, 1 month ago) by pohl
Original Path: branches/Slicer-3-6/Modules/EMSegment/Tasks
BUG: Made EMSegmenter Simple Mode work

Revision 14470 - Directory Listing
Modified Thu Aug 5 00:04:03 2010 UTC (7 years, 2 months ago) by pohl
Original Path: branches/Slicer-3-6/Modules/EMSegment/Tasks
BUG: Reading from disk now works correctly from the commandline module

Revision 14435 - Directory Listing
Modified Tue Aug 3 10:41:48 2010 UTC (7 years, 2 months ago) by pohl
Original Path: branches/Slicer-3-6/Modules/EMSegment/Tasks
BUG: sampling flag was set too low

Revision 14432 - Directory Listing
Modified Tue Aug 3 10:30:47 2010 UTC (7 years, 2 months ago) by pohl
Original Path: branches/Slicer-3-6/Modules/EMSegment/Tasks
ENH: Included Brainsfit in EMSegmenter command line executable

Revision 14205 - Directory Listing
Modified Fri Jul 16 22:26:14 2010 UTC (7 years, 3 months ago) by pohl
Original Path: branches/Slicer-3-6/Modules/EMSegment/Tasks
BUG: Just modified text

Revision 13898 - Directory Listing
Modified Tue Jun 22 11:20:42 2010 UTC (7 years, 4 months ago) by pohl
Original Path: branches/Slicer-3-6/Modules/EMSegment/Tasks
BUG: Correct values are now displayed in registration panel

Revision 13792 - Directory Listing
Modified Mon Jun 14 18:53:25 2010 UTC (7 years, 4 months ago) by pohl
Original Path: branches/Slicer-3-6/Modules/EMSegment/Tasks
BUG: Transfered bug fixes from trunk to 3.6

Revision 13264 - Directory Listing
Modified Thu May 6 14:12:54 2010 UTC (7 years, 5 months ago) by pieper
Original Path: branches/Slicer-3-6/Modules/EMSegment/Tasks
ENH: creating release branche for Slicer-3-6

Revision 13198 - Directory Listing
Modified Tue May 4 01:09:15 2010 UTC (7 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: CommandLine now works and task should be correctly downloaded 

Revision 13165 - Directory Listing
Modified Mon May 3 05:33:35 2010 UTC (7 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Resolving issues around command line module

Revision 13163 - Directory Listing
Modified Sun May 2 22:53:27 2010 UTC (7 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: Fixed EMSegment Simple 

Revision 13117 - Directory Listing
Modified Fri Apr 30 15:45:53 2010 UTC (7 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: removed strange ROI bahavior and registration type bug - Template Builder works now - registration algorithm is still an issue

Revision 13108 - Directory Listing
Modified Fri Apr 30 07:13:41 2010 UTC (7 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
BUG: fixed preprocessing 

Revision 12990 - Directory Listing
Added Wed Apr 28 20:04:57 2010 UTC (7 years, 5 months ago) by pohl
Original Path: trunk/Modules/EMSegment/Tasks
ENH: IBM source code for ARRA project called EMSegmenter

An Exception Has Occurred

Python Traceback

Traceback (most recent call last):
  File &quot;/usr/lib/viewvc/lib/viewvc.py&quot;, line 4844, in main
    request.run_viewvc()
  File &quot;/usr/lib/viewvc/lib/viewvc.py&quot;, line 402, in run_viewvc
    self.view_func(self)
  File &quot;/usr/lib/viewvc/lib/viewvc.py&quot;, line 2950, in view_log
    generate_page(request, &quot;log&quot;, data)
  File &quot;/usr/lib/viewvc/lib/viewvc.py&quot;, line 944, in generate_page
    template.generate(server_fp, data)
  File &quot;/usr/lib/viewvc/lib/ezt.py&quot;, line 329, in generate
    self._execute(self.program, ctx)
  File &quot;/usr/lib/viewvc/lib/ezt.py&quot;, line 458, in _execute
    step[0](step[1], ctx)
  File &quot;/usr/lib/viewvc/lib/ezt.py&quot;, line 466, in _cmd_print
    raise Exception(&quot;Unprintable value type for '%s'&quot; % (str(valrefs[0][0])))
Exception: Unprintable value type for 'logsort_hidden_values'