Not Another Neuroimaging Converter - nanconvert

Brief Description

A set of command-line tools for converting between neuroimaging data formats, using the ITK library for Input/Output, with useful features like writing out diffusion b-value files. Currently supports Bruker 2dseq and limited DICOM (GE flavor).

If you find the tools useful the author would love to hear from you.

Contact

Credit / Blame / Contact - Tobias Wood - tobias.wood@kcl.ac.uk

License

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

Installation

Dependencies & Requirements

1. A C++11 compliant compiler (GCC 4.8.0+, Clang 3.1+)
2. CMake version 2.8.1 or higher (http://www.cmake.org)
3. ITK version 4.13.0 (http://www.itk.org)

Optional - I recommend http://www.ninja-build.org instead of plain make

Compilation

1. Install or compile ITK version 4.13 (as of 2017/11/21, this means compiling the development version.
2. Type the following commands: git clone --recursive https://github.com/spinicist/nanconvert.git cd nanconvert git submodule init; git submodule update
3. Create a build directory and cd to it.
4. Type ccmake path_to_nanconvert_folder
5. Follow the on screen instructions. In particular make sure the path to ITK is specified correctly, then press c and g to configure and generate the build files, then q to quit.
6. Type make -j, and optionally make install (or ninja install)

Usage

The executable nanconvert_bruker can be called to process a single Bruker 2dseq file. Specify the path to the 2dseq file itself, not the folder it resides in. Type nanconvert_bruker -h to see a full list of options.

In addition, the script nanbruker is provided which can convert multiple ParaVision datasets. Type nanbruker to see a full list of options. If nanbruker -q is called, then individual 2dseq files will be converted using jobs submitted to a Sun Grid Engine queue.