Automatic SPHARM Shape Analysis in 3D Slicer
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1 NA-MIC Automatic SPHARM Shape Analysis in 3D Slicer Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner University of North Carolina, Chapel Hill: Neuro Image Research and Analysis Lab NA-MIC Tutorial Contest: Summer 2010
2 Learning Objective Be able to perform shape analysis studies Learn how to: Load input file. Run the ShapeAnalysisModule. Display output scenes.
3 Prerequisites This tutorial assumes that you have already completed the tutorial Data Loading and Visualization. Tutorials for Slicer3 are available at the following location: Slicer3 tutorials
4 Material This tutorial requires the installation of the Slicer3.6 release, BatchMake, some external applications and the tutorial dataset. They are available at the following locations: Slicer3.6 download page: BatchMake download page (BatchMake 1.0.6): External applications download page (spharm-pdm v1.9 Linux32.zip or Linux64.zip ): Tutorial dataset download page (spharm-pdm v1.9 ShapeAnalysis_Data_Example.zip): Disclaimer: It is the responsibility of the user of Slicer to comply with both the terms of the license and with the applicable laws, regulations, and rules.
5 Platform This tutorial has been developed and performed on Linux.
6 Material: External Applications Executables are in spharm-pdm_linux32or64.zip. Download and unzip this file somewhere in your computer. A spharm-pdm_linux32or64 folder will be created, containing executables needed to perform the shape analysis. Executables are: ShapeAnalysisModule, SegPostProcessCLP, GenParaMeshCLP, ParaToSPHARMMeshCLP and MeshMath.
7 Materials: Data Example Download the data locates in ShapeAnalysis_Data_Example.zip. Unzip this file somewhere in your computer. A ShapeAnalysis_Data_Example/origData folder will be created containing two set of binary segmentation of hippocampus. Modify the CSV file, replace the path of the data by your path. e.g: /.../ShapeAnalysis_Data_Example/origData/groupA_01_hippo.gipl.gz The first line of the CSV file, needs to be the headers of the columns.
8 Prerequisites Add the external applications in your PATH: tcsh usage : setenv PATH /../spharm-pdm_linux32or64/:${path} bash usage : export PATH=/../spharm-pdm_linux32or64/:${PATH} Add the BatchMake Applications (two different ways): Add the folder BatchMake_Applications in the same folder as the ShapeAnalysisModule executable. Set the environnement variable BatchmakeShapeAnalysisModule_Dir: tcsh usage : setenv BatchmakeShapeAnalysisModule_Dir /../spharm-pdm_linux32or64/batchmake_applications bash usage : export BatchmakeShapeAnalysisModule_Dir=/../spharm-pdm_linux32or64/BatchMake_Applications
9 Prerequisites Add ShapeAnalysisModule as Slicer3 external module: Open Slicer3. Go to View Application Settings Module Settings. Click on the add a preset button. Select the spharm-pdm_linux32or64 folder and confirm. Close Slicer3.
10 Overview 1- Input file 2- Pipeline description 3- Output images and organisation 4- Execution within Slicer 5- Command line execution
11 Overview 1- Input file 2- Pipeline description 3- Output images and organisation 4- Execution within Slicer 5- Command line execution
12 Input File The input file: Is a CSV file (Comma Separated Value). Contains all the information concerning the subject. e.g: Age, Group, MRI... Contains the path of all the data. e.g: /devel/linux/shapetools/hippocampi/groupa_01.gipl.gz The first line of the CSV file, needs to be the headers of the columns. The data are: A set of binary segmentation of a single brain structure. Fig: a CSV file.
13 Overview 1- Input file 2- Pipeline description 3- Output file and organisation 4- Execution within Slicer 5- Command line execution
14 Pipeline Description Input: CSV file Output: CSV file + MRML scenes
15 Pipeline Description Post Process Segmentation Fills interior holes. Performs minimal smoothing operation and ensures spherical topology. GenParaMesh Processed binary segmentations are converted to raw surfaces meshes. A spherical parametrization is computed. ParaToSPHARMMesh The SPHARM description with inherent correspondence is then computed from the mesh and its spherical parametrization. Triangulated surfaces with correspondences are computed next (SPHARM-PDM) via. icosahedron of the spherical parametrization To get more information about the pipeline: -> MediaWiki
16 Overview 1- Input file 2- Pipeline description 3- Output files and organisation 4- Execution within Slicer 5- Command line execution
17 Output files and organisation A CSV file: Contains all the information from the input file. Contains the path of the output images. Can be use with the UNC statistics module shapeanalysismancova. Three MRML scenes: Scene displayed within Slicer3. Allow the user to visualize all the data on the same scene. Images: Binary 3D Images. Surfaces meshes. Aligned surface meshes.
18 Output files and organisation BatchMake_Scripts/ -ShapeAnalysisModule.bms -ShapeAnalysisModuleMRML.bms Your directory/ Mesh/ Output/ -ShapeAnalysisModule_OutputFile.csv Template/ -same files as SPHARM/ foler PostProcess/ - data.gipl.gz SPHARM/ -data_para.vtk -data_surf_paraphi.txt -data_surf_paratheta.txt -data_surf_para.vtk -data_surfspharm.coef -data_surfspharm_ellalign.coef -data_surfspharm_ellalign.vtk -data_surfspharm_procalign.vtk -data_surfspharm.vtk MRML/ - ShapeAnalysisModuleMRMLScene.mrml - ShapeAnalysisModuleMRMLScene_ellalign.mrml - ShapeAnalysisModuleMRMLScene_procalign.mrml
19 Overview 1- Input file 2- Pipeline description 3- Output files and images 4- Execution within Slicer 5- Command line execution
20 Execution within Slicer 1- Select the ShapeAnalysisModule in Modules ->Shape Analysis. 2- Click on Input File
21 Execution within Slicer 2.1- Select the input file (CSV file) Click on the Open button.
22 Execution within Slicer 1- Select the ShapeAnalysisModule in Modules ->Shape Analysis. 2- Click on Input File. 3- Click on the Output Directory.
23 Execution within Slicer 3.1- Select the output directory Click on the Save button.
24 Execution within Slicer 1- Select the ShapeAnalysisModule in Modules ->Shape Analysis. 2- Click on Input File. 3- Click on Output Directory. 4- Set the enforced spacing in x,y and z direction.
25 Execution within Slicer 1- Select the ShapeAnalysisModule in Modules ->Shape Analysis. 2- Click on Input File. 3- Click on Output Directory. 4- Set the enforced spacing in x,y and z direction. 5- (optionnal) Check the box Label Number and set Value to first extract this label before processing.
26 Execution within Slicer 1- Select the ShapeAnalysisModule in Modules ->Shape Analysis. 2- Click on Input File. 3- Click on Output Directory. 4- Set the enforced spacing in x,y and z direction. 5- (optionnal) Check the box Label Number and set Value to first extract this label before processing. 6- Set Number of Iterations
27 Execution within Slicer 1- Select the ShapeAnalysisModule in Modules ->Shape Analysis. 2- Click on Input File. 3- Click on Output Directory. 4- Set the enforced spacing in x,y and z direction. 5- (optionnal) Check the box Label Number and set Value to first extract this label before processing. 6- Set Number of Iterations. 7- Set the subdivision level for the icosahedron subdivision. 8- Set the maximal degree for the SPHARM computation.
28 Execution within Slicer 1- Select the ShapeAnalysisModule in Modules ->Shape Analysis. 2- Click on Input File. 3- Click on Output Directory. 4. Set the enforced spacing in x,y and z direction before any processing. 5- (optionnal) Check the box Label Number and set Value to first extract this label before processing. 6- Set Number of Iterations. 7- Set the subdivision level for the icosahedron subdivision. 8- Set the the maximal degree for the SPHARM computation. 9- Click on the Apply button to process the data.
29 Execution within Slicer Load the MRML scenes: 1- Click on File -> Load Scene.
30 Execution within Slicer 2- Go in ShapeAnalysis_Results/MRML/ 3- Select one of the three MRML scene 4- Click on the Open button
31 Execution within Slicer
32 Execution within Slicer All the data are displayed with their name.
33 Execution within Slicer Display the color maps: 1. Click on the Snapshots button. 2. Select Color Map Phi or Color Map Theta. 3. Click on Restore.
34 Execution within Slicer Quality Control visualization of the SPHARM correspondence using the color map Phi. Same color represent the same Φ parameter value of the spherical parameterization.
35 Execution within Slicer You can recompute the modules of the ShapeAnalysisModule pipeline. Check one (or more) Overwrite box. Click on the Apply button to recompute the module.
36 Execution within Slicer Input file: By default the first column containing a volume file (.vtk,.meta etc..) is computed. But if you have multiple files in your CSV file, you can choose the column of the input data file. Check the box and enter the column. Post Process Segmentation: You can apply a Gaussian filter. Check the box and set the value of the variance.
37 Execution within Slicer Parameters to SPHARM Mesh: 1. You can choose to set the template (by default the template is the first data computed) Flip template is used to test all possible flips of the parametrization along the first order ellipsoid axis and select the one whose reconstruction has minimal distance to the fliptemplate. Reg template. Mean Template: a mean file is computed and use as a template. ParaOut is use to write The spherical icosahedron subdivision, as well as local phi and theta attribute files for the quality control visualization. 2. You can choose to flip of the parametrization along different axis.
38 Overview 1- Input file 2- Pipeline description 3- Output files and images 4- Execution within Slicer 5- Command line execution
39 Command line execution The module can also be use as a command line tool: ShapeAnalysisModule --sx sy sz label 1 --NumberofIterations SubdivLevelValue 10 --SPHARMDegreeValue 15 --columvolumefile 0 --varx vary 10 --varz 10 --fliptemplate None --regtemplate None --paraouttemplate -- noflip /home/hamelc/shapeanalysismodule/inputfile_shapeanalaysis.csv /home/ha melc/shapeanalysismodule/shapeanalysistest/shapeanalysis_results
40 Conclusion The ShapeAnalysisModule is a 3D Slicer module that allows efficient computation of structural shape analysis via the SPHARM-PDM UNC pipeline including intuitive quality control visualizations. Thanks to this tutorial your are now able to perform shape analysis on your own dataset.
41 Acknowledgments National Alliance for Medical Image Computing NIH U54EB UNC Chapel Hill Neuro Image Research Analysis Laboratories
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