Hello,

I have downloaded the zip file of compiled binaries of spharm-pdm, but I am not sure how to install it into my Linux Ubuntu system as well as add the modules to Slicer3 GUI interface.

Am I supposed to move the binaries to a specific location and make install? Or just add it using the Slicer3 program.

Any help would be greatly appreciated. Thanks!

Sylvia

Hi Sylvia,

In the section Docs/support/Documentation, you will find a tutorial which explain how to install the distribution and how to use ShapeAnalysisModule
You can have the binaries wherever you want : tou are going to specify this location in Slicer3.

Regards,
lucile

Hi Lucile,

Thank you for your speedy response. I am still not able to load the Spharm Module into Slicer3 properly.

I downloaded the spharm-pdm package from the website and extracted the files. I added the external applications in my PATH and added the BatchMake Applications.

Then I opened Slicer3 and added the extracted spharm-pdm folder as a preset under the module settings. Closed the program and opened it again. There were some problems in executing the modules due to the flag characters. I get this message:

ModuleDescriptionParser Error: can only contain one
character. "ap" has more than one character. at line 40 while parsing


Please let me know if I am missing a step somewhere or if there's away to fix that problem. Just for knowing, am I supposed to see a new module named ShapeAnalysis if the executables load properly? Or do I see separate module names (e.g. GenParaMesh, ParaToSPHARMMesh) under Modules in Slicer?

Thanks!

Sylvia

Hi Lucille,

I was able to get the Shape Analysis Module to load in Slicer3 finally by using spharm-pdm v1.9. I tried to use spharm-pdm v1.10.8 on my linux64 OS as well as the v.1.10.7 on my linux32 OS and both didn't load the module.
However, there's still problem loading BatchMake:

Hi Sylvia,

In order to help you, I need you to give me all th errors.
What you can do, is to use the newest realse and try to load it in Slicer and tell me wich modules are not display.
Then you can try to run the module in a terminal with the -xml option. and once again, tell me which module works and the one which not.

Lucile

Hi Lucile,

I have downloaded the newest release for Linux32 which is the 1.10.7 version.

After adding the path of the modules to Slicer3, the only extra modules that show up were bmGridStore, KWMeshVisu, and BatchMake.

The error I received when opening up Slicer3 is:

Starting Slicer: /home/syhon/Slicer3-3.6.3-2011-03-04-linux-x86
OpenGL Warning: Failed to connect to host. Make sure 3D acceleration is enabled for this VM.
ModuleDescriptionParser Error: can only contain one character. "ap" has more than one character. at line 40 while parsing

 
 
 
  BatchMake
 
  1.3.0
  Kitware Inc
 
 
 
 
 
 
  IO
  Input/output parameters

compileScript
compileScript
Compile a script
c


executeScript
executeScript
Execute a script
e


path
path
Specify the batchmake path
p


applicationPath
applicationPath
Specify the path where applications are stored
ap


addApplication
addApplication
Add an application
a


generateShell
generateShell
Generate shell script
sh


generateCondor
generateCondor
Generate condor script
condor


generateGAD
generateGAD
Generate gad script
kwgrid

 


When running each of the external applications through the terminal with the -xml option, this is what I get:
The modules that DO NOT work:
-convertITKformats
-CropImage: error loading libblas.so.3
-GenParaMesh: error loading libblas.so.3
-GenParaMeshCLP: error loading libblas.so.3
-ImageMath: error loading libblas.so.3
-ImageStat
-IVToMeta: error loading libblas.so.3
-KWMeshVisu: error loading libtk8.4.so
-MeshStat: error loading libblas.so.3
-MetaMeshJoiner: error loading libblas.so.3
-MetaStats: error loading libblas.so.3
-MetaToIV: error loading libblas.so.3
-SpharmTool: error loading libblas.so.3
-StatNonParamTestPDM: file does not exist

I am not sure why it's not reading in the libraries. I installed the libraries and the Spharm-pdm package includes the libraries as well.

Thank you.
Sylvia

Hi Sylvia,

Thanks you for all this details. I am going to help you to be able to finaly install this module.

First, I want to tell you that the 32 bits version is not up to date. We have not 32 bits computer available in our lab. It should be soon the case.
But still, you should be able to load the modules.

Can you give me more detail on you OS?

What I understand from your -xml running is that some libraries are not  installed correclty or they are not the good one.
In order to see if you have the good versions of lapackb and blast, you can do a  "ldd path_to_module" in a terminal.
Thus you can verify if you have the correct version installed and also if the paths are the one where you libraries are installed.

If needed, you can try to download (one more time, considering the information of the ldd) those libraries : tcl/tk 8.4, blast and lapack.

Regards,
Lucile

Hi Lucile,

I was able to get my libraries all installed correctly after doing the "ldd" command. So now, I am able to load most modules, I believe; however, I am not sure what I should expect to see. I see the Shape Analysis Module and UNC module where KWMeshVisu falls under. When I click on the Shape Analysis Module, comparing to your powerpoint tutorial, I see everything but the Particles Module, and I am not sure what is the StatNonParamPDM. Am I supposed to see all the modules displayed separately or under Shape Analysis Module?

I am currently Ubuntu11-32bitOS on a VirtualBox.

Thanks!
Sylvia

Hi Lucile,

For the  spharm-pdm_v1.10.8_linux64.zip package, I am trying to install it into my advisor's 64-bit Ubuntu OS. This package includes the particle module, so there would be a lot more required shared libraries.

For some reason, the modules are having difficulty detecting the libraries that are placed in other directories beside in /usr/lib or /lib/ so many of the shared libraries cannot be found. I tried adding the library paths to my PATH, but it did not work. Do you know if there's any easier method to get the libraries to be detected by the modules? Is there any specific bundles of libraries I am supposed to download as well for this newest package?

Thanks for all the help!
Sylvia

Hi Lucile,

Thanks for compiling the Particle Modules for my 32-bit system. I got the shared libraries worked out for the Particle Modules, so the module got loaded into Slicer.

I downloaded the ShapeAnalysisModule_TutorialData package with the hippocampus data to try out the tutorial in your powerpoint. I changed the paths of the data in the CSV file and then when I was just running the Shape Analysis Module, I keep getting the error:

Error: In /extra/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModule/vtkCommandLineModuleLogic.cxx, line 1499
vtkCommandLineModuleLogic (0xde35c00): Shape Analysis Module standard error:

Executing BatchMake Error!
Error: Could not run MeshMath:
No such file or directory
..
..
..
Cannot read the directory /home/syhon/Slicer_Data/tutorialdata/ShapeAnalysisModule_TutorialData/ShapeAnalysis_Results/MRML/Transform Files

I can't seem to output any MRML files. MeshMath seems to be able to execute when I do the --xml option.

Thank you,
Sylvia

Hi

did you set the batchmake directories?

Lucile

Hi Sylvia,
 
I got the same problem as yours. I'm working on Fedora15-64bit OS on a VirtualBox.

I set the environnement variable BatchmakeShapeAnalysisModule_Dir and PATH as the tutorial said. And after adding the ShapeAnalysisModule (spharm-pdm_v1.10.8_linux64.zip) to Slicer3 (Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz), I haven't found the "ShapeAnalysisModule” in the Modules.  The only extra modules that show up were BatchMake, UNC->KWMeshVisu, and bmGridStore.

How did you finally solve this problem?

Thanks,

Xu

  
 Originally posted by Sylvia Hon:

Hi Xu,

I have not completely got the whole tutorial to work, but I got the Shape Analysis Module, Particle Module, as well as the UNC>KWMeshVisu to show up in Slicer.

For each executable, I tested to see if it works. For example, to test GenParaMesh, I did the xml option: ./GenParaMesh --xml
And if it mentions you are missing a shared libraries, you should check which libraries you are missing by doing: ldd module_path  (For example: ldd GenParaMesh  if you are in the module directory)

If you have a problem dealing with shared libraries, this youtube tutorial is helpful: http://www.youtube.com/watch?v=MWpeLdo-3...

Hopefully that will get your modules to show up in Slicer.

Sylvia

Hi Lucile,

I am a bit confused with BatchMake. I compiled BatchMake. When you say "set the batchmake directories" do you mean adding the BatchMake_Applications path to the environment variable BatchmakeShapeAnalysisModule_Dir (like the tutorial pdf)?

I am confused as to what the BatchMake files do, under the BatchMake_Applications folder there are several .bmm files. Am I supposed to alter them?

Thank you.
Sylvia

Hi Sylvia and Xu,

Apparently the compilation of the new binaries was made with the libraries within Slicer. It might be the reason why you have some problems.
I am going to uplaud a new zip version this morning.

Regards,
Lucile.

Hi Lucile,
 
I finally was able to make all the modules show up in slicer using the spharm-pdm_v1.10.9_linux64.zip. However, the whole process still didn't run properly.

( I tested every module separately, and found them working fine except StatNonParamTestPDM, where libitklibxml2.so.3.20 => not found.
I couldn't find this lib file in the itk package and don't know where to get it. )

The slicer gives the following error reports.

 Type: Error
Time: Sun Jun 19 23:44:13 2011
Description: ERROR: In /extra/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1577
vtkCommandLineModuleLogic (0x59ca310): Shape Analysis Module terminated with an unknown exception.
Type: Error
Time: Sun Jun 19 23:44:13 2011
Description: ERROR: In /extra/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1499
vtkCommandLineModuleLogic (0x59ca310): Shape Analysis Module standard error:
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
terminate called after throwing an instance of 'std::length_error'
  what():  basic_string::_S_create


 
Thanks for taking your time to help me.
 
Also thanks Sylvia a lot for sharing the valuable experience with me.
 
Best,
 
Xu. 

Originally posted by Lucile Bompard:

Hi Xu,

I am happy that you succeed, at last, to install the distribution.

We were expecting those issues. The module StatNonParaTestPDM is not up to date. We are now using ShapeAnalysisMANCOVA for the statistical part of the studies.
Considering the problem with CreateMRML, this module needs the Slicer libraries. That the reason why we can not compile it in a static way.
However, the distribution will be soon available as a Slicer extension. Thus, this problem won't exist anymore. However, you can still load the output meshes with the colormap with some software such as KWMeshVisu.

Regards,
Lucile

Hi Lucile,

Thanks for the reply. But I still don't understand why the CreatMRML don't work in the Slicer environment?  Where do these Slicer libraries locate? Or may I download the needed libraries somewhere? 

Best,
Xu
Originally posted by Lucile Bompard:

Hi Lucile,

Thanks for the compilation! I got most of the modules to work beside StatNonParaTestPDM like Xu since i'ts missing some of the shared libraries which I seem to have in my Linux system but I can't seem to add the path using the ldconfig method this tim.

I went over the tutorial once and still cannot create the MRML file because of this error:
ERROR: In
/extra/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx line 1499
vtkcommandLineModulelogic (0x6dd72a0): Shape Analysis Module standard error:

Executing BatchMake: Error!
Error: MeshMath terminated with an exception: Segmentation fault

Do you suggest that I use KWMeshVisu to use the modules instead of Slicer? Do you know when the spharm-pdm extension would be added to Slicer?

Best,
Sylvia

Hi Xu and Sylvia,


In fact we have compiled CreateMRML directly with Slicer. That is to say all the libraries are dynamically linked. That's the reason why  it doesn't find the libraries since there paths correspond to the one we have on our computers.

As Sylvia suggested, you can do the quality control with some software such as KWMeshVisu. But you will only be able to load one mesh.

We are hopping that the spharm distribution will be available as a Slicer extension this summer.We apologize for the inconvenience.


Best,
Lucile

Hi Lucile,

I have been following the tutorial with the hippocampi data with 4 sets of data listed in the input csv. I am having trouble creating the surface mesh of an object and applying the spharm parameterization using Slicer and using the command lines. I am unable to create the ouput csv file, mrml files, nor the .meta files that I see in the processed hippocampi data that was uploaded to this website. In general, I cannot reach the QC/statistics stage.

I am not sure what is preventing the files to be formed. How does your research group or other UNC researchers process the Hippocampi data set?
Should I go through each module (SegPostProcess->GenParaMeshCLP->ParaToSpharmMesh...) instead of using the Shape Analysis Module where it encompasses the other modules?

Thank you for all your prompt responses to my troubleshooting.

Sylvia