tjtaylor/mritools repository overview

⁠docker-mritools

Neurodebian-based MRI Tools

⁠ NeuroDebian

http://neuro.debian.net/index.html⁠

NeuroDebian provides a large collection of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives.

1. Halchenko, Y. O. & Hanke, M. (2012). Open is not enough. Let’s take the next step: An integrated, community-driven computing platform for neuroscience.⁠ Frontiers in Neuroinformatics, 6:22.

⁠ FSL

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL⁠

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslOverview⁠

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. It runs on Apple and PCs (both Linux, and Windows via a Virtual Machine), and is very easy to install. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces). To quote the relevant references for FSL tools you should look in the individual tools' manual pages, and also please reference one or more of the FSL overview papers:

1. M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009

2. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-19, 2004

3. M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012

⁠ Python-Dicom

https://github.com/pydicom/pydicom⁠

https://pydicom.readthedocs.io/en/stable/⁠

pydicom is a pure python package for working with DICOM files. It was made for inspecting and modifying DICOM data in an easy "pythonic" way. The modifications can be written again to a new file. pydicom makes it easy to read these complex files into natural pythonic structures for easy manipulation. Modified datasets can be written again to DICOM format files.

⁠ ITK Convert3D

http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D⁠

https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md⁠

Convert3d is a command-line tool for converting 3D images between common file formats. The tool also includes a growing list of commands for image manipulation, such as thresholding and resampling. The tool can also be used to obtain information about image files.

⁠DCMTK

https://github.com/DCMTK/dcmtk⁠

http://support.dcmtk.org/docs/index.html⁠

This DICOM ToolKit (DCMTK) package consists of source code, documentation and installation instructions for a set of software libraries and applications implementing part of the DICOM/MEDICOM Standard.

⁠DCM2NIIX

https://github.com/rordenlab/dcm2niix⁠

https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage⁠

⁠Build Details

• Debian Version: 17.10

• NeuroDebian Version: nd17.10

• FSL Version: 5.0

• Convert3D Version: 1.1.0

• Python Version: 2.7.14

• Pydicom Version: 0.9.9

• DCMTK Version: 3.6.2

• DCM2NIIX Version: 1.0.20171103