2010 Winter Project Week SPECTRE 3DSlicer Integration - Revision history

Naucoin: /* Trouble shooting */

2010-10-29T15:36:37Z

Trouble shooting

2010-10-29T15:27:00Z

Trouble shooting

2010-10-29T15:20:33Z

Build and install SPECTRE as an extension module for a prebuilt binary of Slicer3

2010-10-28T22:43:06Z

Trouble shooting

2010-10-28T22:00:07Z

Trouble shooting

2010-10-28T21:58:35Z

Trouble shooting

2010-10-28T21:47:51Z

Build and install SPECTRE as an extension module for a prebuilt binary of Slicer3

2010-10-28T19:00:37Z

Build and install SPECTRE as an extension module for a prebuilt binary of Slicer3

2010-10-28T18:42:38Z

October 2010

2010-10-26T22:14:40Z

October 2010

@@ Line 153: / Line 153: @@
 ** download the L-M fit package http://users.utu.fi/jaolho/ and unzip it in toads-cruise/releases/spectre/jistCRUISE/JIST
 ** comment out all references to the missing class edu.jhu.ece.iacl.algorithms.graphics.utilities.GeodesicNeighborsOnSurface in the file jistCRUISE/JIST/src/edu/jhu/ece/iacl/algorithms/graphics/utilities/SurfaceMetrics.java
 * Use make, make clean, make install to rebuild without the extend.tcl script
 * After compiling try running the tests:
@@ Line 182: / Line 184: @@
 ** When tclsh SPECTRE.tcl is run with the --xml flag, nothing can be printed to standard output before <?xml or the module will not be recognised as a plugin
 * The Mask output volume isn't loaded as a label map, you can reset it in the Volumes module, Info pane
 * The output volumes will sometimes have a flipped orientation, you can fix it in Slicer by:
 ** In the Data module, right click on Scene and Add Transform

@@ Line 150: / Line 150: @@
 * If the SPECTRE building step fails with an error about not being able to find MIPAV, add the path to mipav to your PATH environment variable
 * After compiling try running the tests:
    cd Slicer3-ext/SPECTRE-build
@@ Line 159: / Line 163: @@
 * Look in fileError.txt (standard error is written to this file)
 ** if there's an error similar to:cli	PARSE Error: Invalid ProcessingAlgorithm: edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2009
-** then run MIPAV to set up some defaults. Instructions from Min:
+** then run MIPAV to set up some defaults (you may have to do this more than once if you're re-compiling). Instructions from Min:
 <pre>
 .)Close out of everything
@@ Line 176: / Line 180: @@
 </pre>
 * If the SPECTRE module doesn't load into Slicer, exit and restart it with the --verbose-module-discovery command line option and look in the error log to see what was reported about the module discovery process for SPECTRE.tcl (the wrapper script for the .jar file)
 ===January 2010===

@@ Line 134: / Line 134: @@
 * Under View->Application Settings go to the Module Settings page
 ** add a directory pointing to the location of SPECTRE.tcl
-* Restart Slicer3 and look for the new plugin uner Modules->Developer Tools
+* Restart Slicer3 and look for the new plugin under Modules->Developer Tools
 ====To run SPECTRE:====

@@ Line 153: / Line 153: @@
    cd Slicer3-ext/SPECTRE-build
    ctest -R SPECTRE -VV
-* Try running it manually, the following command should print out the XML description of the parameters
+* Try running it manually, the following command should print out the XML description of the parameters with '''nothing''' before <?xml (otherwise Slicer won't recognise it as a plugin)
    tclsh ./SPECTRE.tcl --xml
 * If the XML is not printed out, you can try passing a bogus argument to see what the class path settings are (look for the path to MIPAV to verify that it's picking up the correct version)
    tclsh ./SPECTRE.tcl --bogus
-* Look in fileError.txt
+* Look in fileError.txt (standard error is written to this file)
 ** if there's an error similar to:cli	PARSE Error: Invalid ProcessingAlgorithm: edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2009
 ** then run MIPAV to set up some defaults. Instructions from Min:

@@ Line 158: / Line 158: @@
    tclsh ./SPECTRE.tcl --bogus
 * Look in fileError.txt
-** if there's an error like the following, try running MIPAV
+** if there's an error similar to:cli	PARSE Error: Invalid ProcessingAlgorithm: edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2009
-  cli	PARSE Error: Invalid ProcessingAlgorithm: edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2009
+** then run MIPAV to set up some defaults. Instructions from Min:
 <pre>
 .)Close out of everything

@@ Line 149: / Line 149: @@
 ====Trouble shooting====
-* Compiling:
+* If the SPECTRE building step fails with an error about not being able to find MIPAV, add the path to mipav to your PATH environment variable
-** if the SPECTRE building step fails, add the path to mipav to your PATH environment variable
+* After compiling try running the tests:
-** you'll have to run MIPAV once to set up some defaults, from Min:
+  cd Slicer3-ext/SPECTRE-build
 <pre>
 .)Close out of everything
@@ Line 167: / Line 176: @@
 .)Try running it in Slicer again
 </pre>
 * If the SPECTRE module doesn't load into Slicer, exit and restart it with the --verbose-module-discovery command line option and look in the error log to see what was reported about the module discovery process for SPECTRE.tcl (the wrapper script for the .jar file)

@@ Line 127: / Line 127: @@
 * Build
    gmake
-* If the build succeeds, there should be two important files in SPECTRE_Plugin/SPECTRE-install
+  make install
    SPECTRE.tcl
    SPECTRE_Slicer.jar

@@ Line 119: / Line 119: @@
 * c to configure
 * Set any missing values
-**MIPAV should point to your installed version of mipav
+**MIPAV should point to your installed version of mipav: SPECTRE_Plugin/mipav
-  SPECTRE_Plugin/mipav
+**You can point the SPECTRE_ATLAS_TXT to the downloaded atlas: SPECTRE_Plugin/spectre_atlases/oasis-3.txt
-**You can point the SPECTRE_ATLAS_TXT to the downloaded atlas
+**CMAKE_INSTALL_PREFIX to SPECTRE_Plugin/SPECTRE-install
 * c to configure
 ** if it complains about not finding the INPUT_AXIAL_SUBSAMPLE file, c again or set it if you have a test image
@@ Line 128: / Line 127: @@
 * Build
    gmake
-* If the build succeeds, there should be two important files
+* If the build succeeds, there should be two important files in SPECTRE_Plugin/SPECTRE-install
    SPECTRE.tcl
    SPECTRE_Slicer.jar

@@ Line 84: / Line 84: @@
 * Install MIPAV 5.0.0 or later
 ** set the install directory on linux to be Slicer3-lib/mipav. The default c:/Program Files/ location on windows should be fine.
 * Download the extension file [http://wiki.na-mic.org/Wiki/index.php/File:SPECTRE.s3ext.gz SPECTRE.s3ext.gz]
 ** use gunzip to expand it
@@ Line 117: / Line 100: @@
 * Restart Slicer3
 * Look for the new module under Modules, Developer Tools, SPECTRE2009
 ====To run SPECTRE:====
@@ Line 131: / Line 149: @@
 ====Trouble shooting====
 * After compiling try running the tests:
    cd Slicer3-ext/SPECTRE-build