NIRALUser / DTIAtlasBuilder

This tool creates an Atlas image as an average of several DTI images that will be registered

DTIAtlasBuilder

Current stable release: 1.6.4 (06/27/2020)

What is it?

A tool to create an atlas from several DTI images

Where is it?

Find the tool on NITRC and GitHub

Binary package available on the NITRC download page

Usage tutorial available from NITRC

External Requirements

Following OS level library and tools needs to be installed before build

• python-devel
• qt4-qtbase-devel
• qt5-qtbase-devel
• freeglut-devel
• cmake 3.4 or above

These Softwares need to be installed before executing the tool :

• ImageMath
• ResampleDTIlogEuclidean
• CropDTI
• dtiprocess
• BRAINSFit
• GreedyAtlas
• dtiaverage
• DTI-Reg
• MriWatcher
• unu

If you do not have these softwares installed on your machine, you can use the COMPILE_PACKAGE CMake option to download and compile aumatically the tools you need. If you do so, please run "make install" after the compilation to copy the tools into the CMAKE_INSTALL_PREFIX.

Dockerfile for developers

Use below command in source directory to build docker image (Currently having only CentOS7 image.

$ docker build . -t <image-name>
$ docker run --rm -it -v $PWD/../:/work -w /work <image-name> 

Change Log:

v1.6.4a (07/26/2020)

• json related conversion ambiguity resolved.
• glut is not going to be build. Freeglut needs to be installed as described in Dockerfile
• OSX build bug fixed.

v1.6.4 (06/27/2020)

• DTIAtlasBuilderResults.csv is now being generated for all the sub atlases
• DTIAtlasBuilderResults.csv for the concatenated displacement fields is generated in the project root directory with the same name. This file has the original images' paths, the first level intermediate files and the concatenated displacement field file path from the final atlas to the individual images.

v1.6.3 (06/08/2020)

• Parallel build using multithread enabled (Change the number of thread to use in Software configuration tab)
  • Desirable usage : set the number of thread whose multiple is equal to the number of end-nodes to maximize the parallelism

v1.6.1-beta1 (06/01/2020)

• New action in file menu added : Open Project Directory, which loads all the parameters and hierarchy from an existing project directory
• New action in tool menu added : Generate Project Directory, which generates all the necessary files for the project and doesn't execute the script.
• Generation of deformation fields track file for the concatenation by ITKTransformTools
• Concatenation of deformation fields from hierarchical atlas structure.

v1.6.0 (05/28/2020)

• Hierarchical atlas build has been implemented.
• Treeview implemented for GUI users to generate the hierarchy.
• Deformation field track file is generated for the concatenation over multiple level atlas build.
• MriWatcher can view the final atlases for QC.
• DTIAtlasBuilderParameters.txt now has version 4, where iteration over final resampling is added and dataset csv file field is removed.
• ITKTransformTools is added to the installation binary directory as a tool for the concatenation of deformation fields
• Project directory scaffolding has been changed to 'atlases','final_atlas','common','scripts'

v1.5.2 (04/20/2020)

• Final Atlas will be copied into 5_Final_Atlas directory once completed

v1.5.1 (04/09/2020)

• Superbuild pattern renewed
• Scripts are now extracted into independent python codes. Hard coded scripts are no more to be used.
• JSON incorporated
• Final resampling iteration implemented
• Automatic cleanup for intermediate files in final resampling steps

v1.5 (11/12/2018)

• Fix superbuild mechanism for SlicerExtension
• New mechanism to find executables based on Slicer architecture

v1.3 (06/26/2013)

• File/Folder management:

  • Keep original subject names instead of using "CaseX"
  • Put final files in specific folders (FinalTensors and FinalDeformationFields)
  • Automatically update files/folders names if running DTIAtlasBuilder over a previous computation done with an older version

• Add step at the beginning to filter and set to zero negative values in tensors to avoid issues in registration

• New Interface features:

  • Drag & Drop images and text files (CSV, parameters and software configuration files)
  • "Clean output folder" button
  • Keyboard shortcuts
  • Remove duplicated cases
  • Improve enable/disable buttons

• Other minor bug fixes

• Python version 2.5 minimum required

v1.2 (05/01/2013)

• Fixing the output global displacement fields when using ANTs

• Files/Folders name changes:

2_NonLinear_Registration/CaseX_DeformationField.mhd                     -> 2_NonLinear_Registration/CaseX_HField.mhd
4_Final_Resampling/First_Resampling/CaseX_GlobalDeformationField.nrrd   -> 4_Final_Resampling/First_Resampling/CaseX_GlobalDisplacementField.nrrd
4_Final_Resampling/Second_Resampling/CaseX_GlobalDeformationField.nrrd  -> 4_Final_Resampling/Second_Resampling/CaseX_GlobalDisplacementField.nrrd

v1.1 (02/22/2013)

• Add a SuperBuild system to automatically download and compile all needed external tools

• Add DTIAtlasBuilder as a Slicer extension

• Replace AtlasWerks by GreedyAtlas

• Files/Folders name changes:

2_NonLinear_Registration_AW                  -> 2_NonLinear_Registration
2_NonLinear_Registration/AverageImage.mhd    -> 2_NonLinear_Registration/MeanImage.mhd
3_AW_Atlas                                   -> 3_Diffeomorphic_Atlas
3_Diffeomorphic_Atlas/CaseX_AWDTI.nrrd       -> 3_Diffeomorphic_Atlas/CaseX_DiffeomorphicDTI.nrrd
3_Diffeomorphic_Atlas/AWAtlasDTI.nrrd        -> 3_Diffeomorphic_Atlas/DiffeomorphicAtlasDTI.nrrd

v1.0 (10/11/2012)

• Initial version

Troubleshooting:

Final Atlas is bad

If you see in the QC windows that the Affine and Diffeomorphic Atlases and registered images look OK, and that the Final Atlas and images look bad for all or most cases, that means that something went wrong during the FINAL registration.
If this final registration was done using BRAINS, try to recompute it using ANTS (in the Final Resampling tab > Registration Method), which gives a better registration.

Loading parameter file fail

If a parameter file fails to open in DTIAtlasBuilder (Parameter file is corrupted), you need to recreate it by loading only the corresponding dataset file and setting your options again.

QC does not show up

If the QC windows do not appear when pushing the QC buttons, it might mean that you need to install the GLUT library to get MriWatcher to work.
You can find the GLUT library here

Contact : jprieto[at]med.unc.edu

Slicer extension build status: Open the dashboard and search "DTIAtlasBuilder" in the build name using the filters.