Ferraris, S; Shakir, DI; Van Der Merwe, J; Gsell, W; Deprest, J; Vercauteren, T; (2017) Bruker2nifti: Magnetic Resonance Images converter from Bruker ParaVision to Nifti format.Journal Of Open Source Software, 2 (16) p. 354. 10.21105/joss.00354.
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Abstract
- Data conversion for MRI analysis¶ Most MRI analysis applications do not work well with DICOM data so it is generally necessary to convert your data to a friendlier format such as nifti (.nii) or MRtrix format (.mif). Depending on what you are doing there are several ways to do this.
- Tkmedit -f /path/to/your/file.mgz Example Usage: tkmedit -f./mri/T1.mgz Converting FreeSurfer result files (.mgz) to NIFTI. We use mriconvert utility. You may need to change -outorientation parameter if your nifti files come up in a wrong orientation.
第二十二期 fNIRS Journal Club 通知 2021/08/28，10:00am 美国南卡罗来纳大学心理学系的符晓雪博士，将为大家讲解她刚刚发表在Neurophotonics上的一篇文章，用NIRS研究发育过程中头皮和大脑关系的变化。.
In clinical and pre-clinical research involving medical images, the first step following a Magnetic Resonance Imaging dataset acquisition, usually entails the conversion of image data from the native scanner format to a format suitable for the intended analysis. The proprietary [Bruker ParaVision](https://www.bruker.com/products/mr/preclinical-mri/software/service-support.html) software currently does not provide the tools for conversion of the data to suitable and open formats for research, such as nifti [@cox2004sort], for which most of the available tools for medical image analysis are implemented. For this purpose we have designed and developed [bruker2nifti](https://github.com/SebastianoF/bruker2nifti), a pip-installable Python tool provided with a Graphical User Interface to convert from the native MRI Bruker format to the nifti format, without any intermediate step through the DICOM standard formats [@Mildenberger2002]. Bruker2nifti is intended to be a tool to access the data structure and to parse all parameter files of the Bruker ParaVision format into python dictionaries, to select the relevant information to fill the Nifti header and data volume. Lastly it is meant to be a starting point where to integrate possible future variations in Bruker hardware and ParaVision software future releases.
| Type: | Article |
|---|---|
| Title: | Bruker2nifti: Magnetic Resonance Images converter from Bruker ParaVision to Nifti format |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.21105/joss.00354 |
| Publisher version: | http://dx.doi.org/10.21105/joss.00354 |
| Language: | English |
| Additional information: | Authors of JOSS papers retain copyright and release the work under a Creative Commons Attribution 4.0 International License (CC-BY) (http://creativecommons.org/licenses/by/4.0/). |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Med Phys and Biomedical Eng |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1571768 |
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Freesurfer Dicom To Nifti
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