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| [](https://doi.org/10.5281/zenodo.3818614) | ||
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| # BrkRaw: Comprehensive tool to access Bruker PV dataset | ||
| ## Version: 0.3 | ||
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| ### Description | ||
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| The 'BrkRaw' python module is designed to be a more comprehensive tool for the preclinical MRI community for accessing and | ||
| utilizing raw data. And since the converter is front-line tools for medical imaging, the functionality is developed to cover | ||
| the requirements from the various user, including MRI system operator, maintainer, MR sequence developer, imaging researcher, | ||
| and data scientist. In addition to these, we had put extra efforts to preserve the metadata as well as provide tools to help | ||
| organize the data structure into a shareable format that suggested from the open science community for pursuing | ||
| reproducible science [BIDS](https://bids.neuroimaging.io). Therefore, the module designed not only can be used for the NifTi converter, | ||
| but also provides command-line tools and python API for previewing, organizing and archiving data, and parsing metadata, | ||
| accessing the data as users convenient object type ([nibabel](https://nipy.org/nibabel/) or | ||
| ## BrkRaw: A comprehensive tool to access raw data of Bruker Biospin Preclinical MRI Systems | ||
| #### Version: 0.3.3 | ||
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| #### Description | ||
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| The ‘BrkRaw’ is a python module designed to provide a comprehensive tool to access raw data acquired from | ||
| Bruker Biospin preclinical MRI scanner. This module is also compatible with the zip compressed data | ||
| to enable use of the archived data directly. | ||
| The module is comprised of four components, including graphical user interface (GUI), command-line tools, | ||
| high-level and low-level python APIs. | ||
| - For the GUI, we focused on improving convenience for checking metadata and previewing the reconstructed image. | ||
| - For the command-line tool, we focused on providing tools for converting, organizing, archiving, and managing data. | ||
| The command-line tool also provides easy-to-use function to convert large set of raw data into organized structure | ||
| according to [BIDS](https://bids.neuroimaging.io). | ||
| - For the high-level python API, we focused on enhancing the accessibility of reconstructed image data with | ||
| preserved image orientation and metadata for the image analysis. | ||
| It compatible users' convenient objects type ([nibabel](https://nipy.org/nibabel/) or | ||
| [SimpleITK](https://simpleitk.readthedocs.io/en/master/gettingStarted.html#python-binary-files)) | ||
| without the conversion step. The module is compatible with the ZIP file format, so no need to uncompress the file to access data. | ||
| The goal of this project is providing easy-to-access of the Bruker's PVdatasets. | ||
| The major features of this module are as follows. | ||
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| - Reliable converting function with | ||
| - preserving the subject position and orientation to converted the NifTi1 file. | ||
| - correction of animal orientation based on the species and position. (Anterior of subject is Anterior). | ||
| - providing fMRI and DTI study friendly features: slice-order update on the header, Diffusion parameter file generation. | ||
| - BIDS(v1.2.2) support: parameter file generation with custom syntax, automatic generation of the folder structure. | ||
| - Capability of quick image validation by | ||
| - providing the GUI tool for preview the dataset without conversion. | ||
| - the command-line tool function for previewing metadata of the dataset for each scan. | ||
| - Data management tool 'brk-backup' | ||
| - Data management tool 'brk-backup' for archiving and performing inspection the backup status. | ||
| - Robust and easy-to-use python API for developers, including JCAMP-DX parser. | ||
| - Object-oriented robust dataset parser. | ||
| - compressed data readability (compatible with .zip and .PVdatasets format). | ||
| - the python API also providing data handler object through either nibabel and simpleITK to make convenient to the researcher can implement their own code. | ||
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| ### Update notes: | ||
| ##### BrkRaw v0.3.2 | ||
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| 1. Improved BIDS converter. | ||
| - Bruker FieldMap will be accommodated into the BIDS excel sheets. With new feature, bids_converter separates fieldmap and magnitude image. | ||
| - Multi-echo sequenced data will be converted as separate format. | ||
| 2. Bug patches. | ||
| - GUI visualization or crash issues related to certain conditions are patched. | ||
| - Matrix size instability has been patched, except multi-echo, all data will be converted to 3D + frame | ||
| - DTI slope correction issue is patched. | ||
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|  | ||
| **Fig1.** Example subject alignment shown on FSLeyes, the overlayed localizer image for each slice axis(gray) and a EPI image(red) are align in the same space while the preserve subject orientation (correct R-L, I-S, A-P on rodent) | ||
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| ### Compatibility | ||
| - Cross-platform compatibility (OSX, Linux, Windows 10) | ||
| - Best work on Python 3.7.6, does not support Python 2. | ||
| - Dependency: shleeh>=0.0.4, nibabel>=3.0.2, SimpleITK>=1.2.4, | ||
| numpy>=1.18.0, pandas>=1.0.0, pillow>=7.1.1, | ||
| tqdm>=4.45.0, openpyxl>=3.0.3, xlrd>=1.0.0 | ||
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| ### Installation | ||
| - We are highly suggesting to use **Python 3.7** | ||
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| #### Requirement | ||
| - The installed Python must be compiled properly, | ||
| If you use pyenv and are having any issue with python please refer following link: | ||
| [Common Build Problems in PyENV](https://github.com/pyenv/pyenv/wiki/common-build-problems) | ||
| - To use gui feature, the installed python should compiled with tkinter module. | ||
| - You can test the tkinter installation with below command on your shell. | ||
| ```angular2html | ||
| $ python -m tkinter -c 'tkinter._test()' | ||
| ``` | ||
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| - In Mac OSX, Homebrew installed tcl-tk and pyenv may have an issue with tkinter, please refer following link to solve the issue: | ||
| [Issue with Homebrew installed tcl-tk on pyenv](https://github.com/pyenv/pyenv/issues/1375) | ||
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| #### Install via PyPI | ||
| ```angular2html | ||
| $ pip install bruker | ||
| ``` | ||
| without the conversion step. | ||
| - For the low-level python API, we focused on providing a consistent method to access raw Bruker data including | ||
| parameter and binary files with the python compatible datatype while keeping the sake of simplicity. | ||
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| #### Install via Github | ||
| ```angular2html | ||
| $ pip install git+https://github.com/dvm-shlee/bruker | ||
| ``` | ||
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| #### Conversion reliability | ||
| ##### Conversion reliability | ||
|  | ||
| **We've tested our converter using the sample dataset from [Bruker2Nifti_QA](https://gitlab.com/naveau/bruker2nifti_qa) | ||
| and the results showed correct geometry and orientation for all datasets.** | ||
| - We are still looking for more datasets showing orientation issue, if you have any shareable dataset, please contact | ||
| author. | ||
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| #### Known issues | ||
| - The converter has not been tested the Paravision 360 | ||
| - Most of the GUI issues could be related to tkinter, please follow the above instruction first before open a issue. | ||
| - Few update committed since the first stable version release, if you have any issue, please try the latest version. | ||
| - For other unexpected issues, please use the issue channel. | ||
| - There will be potential bug that occurred with new version updated, please let developer knows those issue by openning | ||
| issue channel. Thank you for your contribution! | ||
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| ## Usage | ||
| ### Command-line tool (brkraw) | ||
| #### Quick access of metadata | ||
| - Printing out dataset information | ||
| ```angular2html | ||
| $ brkraw summary <session path or compressed dataset> | ||
| ``` | ||
|  | ||
| **Example of printed out dataset information** | ||
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| #### The Legacy version of NifTi1 conversion | ||
| - This method has been inherited from old brk2nii and [PyBruker](https://pypi.org/project/pyBruker) which | ||
| has been removed from repository and is not existing anymore. This function is useful if you want to convert | ||
| whole dataset without need to considering data structure, or only needs to convert specific scan and reco. | ||
| - Convert a whole session, (adding option '-b' or '--bids' will generate JSON file that contains MR parameters | ||
| based-on BIDS standard) | ||
| ```angular2html | ||
| $ brkraw tonii <session path or compressed dataset> | ||
| ``` | ||
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| - Convert a scan, (default reco_id is 1) | ||
| ```angular2html | ||
| $ brkraw tonii <session path or compressed dataset> -s <scan id> -r <reco id> | ||
| ``` | ||
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| - Build BIDS dataset with multiple Bruker raw datasets. | ||
| - You need to copy all data into one parent folder, compressed zip file will also work (we recommend to use zip file) | ||
| - All dataset under parent folder will be converted into ./Data folder with BIDS structure, but filename will not follow | ||
| the BIDS standard. If you need to share your data, we recommend to use bids_converter function instead. | ||
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|  | ||
| **Example of automatically generated BIDS dataset** | ||
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| ```angular2html | ||
| $ brkraw tonii_all <parent folder> | ||
| ``` | ||
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| #### Automatic BIDS organizer with template files | ||
|  | ||
| **The usage of the command-line tool 'brkraw' for BIDS data organization.** | ||
| We've tested our converter using the sample dataset from [Bruker2Nifti_QA](https://gitlab.com/naveau/bruker2nifti_qa) | ||
| and the results showed correct geometry and orientation for all datasets. | ||
| We are still looking for more datasets showing orientation issue, | ||
| **if you have any shareable dataset, please contact the developer.** | ||
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| - Upgraded feature to reduce the burden on renaming according to BIDS standard. | ||
| - Create a BIDS file table with excel format to use as a template for updating metadata | ||
| that required to use for file naming. | ||
| - This command will also generate the BIDS_META_REF.json which allows you to set | ||
| custom syntax to parse the metadata from the rawdata. The default reference of | ||
| the current version is based on BIDS 1.2.2. | ||
| - The bids_converter command will also generate empty template of `dataset_description.json` and `README` | ||
| - To learn more detail, please check our example | ||
| [Jupyter Notebooks](https://github.com/dvm-shlee/bruker/blob/master/examples/BrkRaw_PythonAPI.ipynb). | ||
| ```angular2html | ||
| $ brkraw bids_list <parent folder> <filname>.xlsx | ||
| ``` | ||
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| - Build BIDS dataset according to the excel file generated with 'bids_list' command above. | ||
| ```angular2html | ||
| $ brkraw bids_converter <parent folder> <BIDS table file.xlsx> | ||
| $ brkraw bids_converter <parent folder> <BIDS table file.xlsx> -r <BIDS meta reference file.json> | ||
| ``` | ||
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| - Run GUI with input and output path | ||
| ```angular2html | ||
| $ brkraw gui -i <session path> -o <output path> | ||
| ``` | ||
|  | ||
| **brkraw gui interface.** | ||
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| - You can run GUI without any path option. It will show you only two buttons (Open File / Open Directory). | ||
| In case you are opening zipped PVdataset, please use 'Open File' button. For later case, | ||
| Make sure you are entered to the PVdataset root folder where the subject file located. | ||
| If you does not enter to the dataset folder, the GUI will freeze. This case, just force quit the GUI. | ||
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| ```angular2html | ||
| $ brkraw gui | ||
| ``` | ||
| #### Website | ||
| For more detail information including installation, usage and examples, | ||
| please visit our [GitPage](https://brkraw.github.io). | ||
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| ### Data management tool | ||
|  | ||
| **brk-backup script utilizing the Python API to immediately access both raw data and archived data | ||
| to parse the metadata for data management.** | ||
| - [Installation](https://brkraw.github.io) | ||
| - [Command-line tool usage examples](https://brkraw.github.io) | ||
| - [Converting dataset into BIDS](https://brkraw.github.io) | ||
| - [Python API usage examples](https://brkraw.github.io) | ||
| - [GUI](http://brkraw.github.io) | ||
| - [How to contribute BrkRaw](https://brkraw.github.io) | ||
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| - Print out archived dataset and its condition | ||
| ```angular2html | ||
| $ brk-backup archived <rawdata path> <backup path> | ||
| $ brk-backup archived <rawdata path> <backup path> -l // generate log file instead of printing | ||
| ``` | ||
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| - Print out review backup status | ||
| ```angular2html | ||
| $ brk-backup review <rawdata path> <backup path> | ||
| $ brk-backup review <rawdata path> <backup path> -l // generate log file instead of printing | ||
| ``` | ||
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| - Archive data from rawdata path to backup path, if the dataset has been archived and identical, then skip | ||
| ```angular2html | ||
| $ brk-backup backup <rawdata path> <backup path> | ||
| ``` | ||
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| - Remove files classified as unnecessary via review process among backed up data. The interactive UI will ask you | ||
| to confirm each step to prevent erase important data | ||
| ```angular2html | ||
| $ brk-backup clean <rawdata path> <backup path> | ||
| ``` | ||
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| #### Windows 10 | ||
| - Same as above, but use brkraw.exe instead of brkraw command. | ||
| - If this command is not working, please check the version of your Anaconda and Python. | ||
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| #### Python API | ||
| - import module | ||
| ```angular2html | ||
| >>> import brkraw | ||
| ``` | ||
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| - load dataset | ||
| ```angular2html | ||
| >>> rawdata = brkraw.load(<PATH>) | ||
| ``` | ||
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| - For more detail, Please check out our | ||
| [Jupyter Notebooks](https://github.com/dvm-shlee/bruker/blob/master/examples/BrkRaw_PythonAPI.ipynb) | ||
| in the example directory. | ||
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| ### Contributing | ||
| - Please contact [email protected] if you interest to contributing in this project any direction. | ||
| 1. Improve BIDS organization | ||
| 2. Develop documentation or tutorials for below items using our Python API. | ||
| - FieldMap correction, reconstruction (integrate BART tool), acute quality control, fMRI and DTI analysis | ||
| - **if you experience any bug or have any suggestion to improve this tool, please let us know.** | ||
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| ### Credits and roles: | ||
| #### Authors | ||
| #### Credits: | ||
| ##### Authors | ||
| - SungHo Lee ([email protected]): main developer | ||
| - Woomi Ban ([email protected]): sub-developer who tested and refined the module structure | ||
| - Yen-Yu Ian Shih ([email protected]): technical and academical advisory on this project (as well as funding) | ||
| #### Contributors | ||
| ##### Contributors | ||
| - Drs. Chris Rorden and Sebastiano Ferraris: The pioneers related this project who had been inspired the developer | ||
| through their great tools including [dcm2niix](https://github.com/rordenlab/dcm2niix) and | ||
| [bruker2nifti](https://github.com/SebastianoF/bruker2nifti), as well as their comments to improve this project. | ||
| - Drs. Mikael Naveau and Gabriel A. Devenyi: The publisher of | ||
| [bruker2nifti_qa](https://gitlab.com/naveau/bruker2nifti_qa), the set of data | ||
| to help benchmark testing of Bruker converter. | ||
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| ### How to Cite | ||
| #### License: | ||
| GNU General Public License v3.0 | ||
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| #### Citing BrkRaw | ||
| SungHo Lee. (2020, May 13). dvm-shlee/bruker: BrkRaw v0.3.2 (Version 0.3.2). Zenodo. http://doi.org/10.5281/zenodo.3818614 | ||
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| **BibTeX** | ||
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@@ -260,17 +73,3 @@ SungHo Lee. (2020, May 13). dvm-shlee/bruker: BrkRaw v0.3.2 (Version 0.3.2). Zen | |
| url = {https://doi.org/10.5281/zenodo.3818614} | ||
| } | ||
| ``` | ||
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| ### Acknowledgements | ||
| We thank to the researchers of the Rorden lab at the University of South Carolina, | ||
| especially Drs. Chris Rorden and Sebastiano Ferraris, regarding their pioneer works and sharing excellent tools | ||
| for raw data conversion to the community that inspired the first author of this project, | ||
| as well as their sharing know-how. We also thank Dr. Mikael Naveau at Cyceron and Gabriel A. Devenyi | ||
| at Douglas Mental Health University Institute who shared the dataset for benchmarking converter. | ||
| Lastly, We thank to the staff and colleagues in the Center for Animal MRI (CAMRI) | ||
| at the University of North Carolina at Chapel Hill for the testing and providing helpful feedback. | ||
| Especially thanks to Ms. Tzu-Wen Wang for the test the tool at the front-line. | ||
| This work was supported by NIH (Grant No: RF1MH117053, R01MH111429, and R01NS091236). | ||
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| ### License: | ||
| GNU General Public License v3.0 | ||
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| from .lib import * | ||
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| __version__ = '0.3.2' | ||
| __version__ = '0.3.3rc0' | ||
| __all__ = ['BrukerLoader', '__version__'] | ||
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