NIfTI

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Welcome to the NIfTI & GIfTI page. NIfTI and GIfTI are standardized file formats for the neuroimaging community for volumetric resp. surface-based data.

Contents

News

The wiki will be migrated to the new BrainVoyager support site.

For NIfTI plugins for BrainVoyager QX 2.0, see the NIfTI page on the support site: http://support.brainvoyager.com/index.php?option=com_content&view=article&id=166:nifti-conversion-volumetric-files&catid=49:available-plugins&Itemid=26 (Latest update: 22-06-09).

For GIFTI plugins for BrainVoyager QX 2.0, see the GIFTI page on the support site: http://support.brainvoyager.com/index.php?option=com_content&view=article&id=158:gifti-conversion&catid=49:available-plugins&Itemid=26 (Latest update: 22-06-09).


NIfTI

Introduction

NIfTI-1 is a file format designed by and for the neuroimaging community. This has been performed by software developers or their representatives in a Data Format Working Group (DFWG), supported by the NIH (see http://nifti.nimh.nih.gov/nifti-1/). Chair is Stephen Strother. The NIfTI-1 format is a successor of the Analyze 7.5 format and it is kind of backwards compatible. BrainVoyager QX is NIfTI-1.0 compliant via the nifti converter plugin that can be downloaded below. Soon it will be NIfTI-1.1 compliant.

Documentation

Plugin documentation:
Here is the niftiplugin design (v0.6) (Latest update: 28-Apr-09).
This is the niftiplugin manual (v0.6) (Latest update: 21-Aug-08).
Here is the niftiplugin API (code will follow) (Latest update: 07-Apr-08).

For documentation on the NIfTI-1 format that evolved from Analyze 7.5, please have a look at the NIfTI website at http://nifti.nimh.nih.gov/ or the website.

NIfTI format documentation:
NIfTI-1 documentation (*.pdf) The NIfTI-1 format, explained by R.W. Cox and M. Jenkinson (and drawings by me, Hester Breman).
NIfTI codes: intent and extension codes (will be updated soon).
NIfTI format documentation in the documentation for the plugin version 1.04:
NIfTI-1 documentation for Windows (*.chm)
platform-independent NIfTI-1 documentation (FlashHelp)

Tools

plugin versions

Please find below a kind of cross-platform NIfTI-1 converter. It is regularly updated with a BrainVoyager QX data format that can be imported, exported or both. It can also be used to view header information or to save the header information in a text file (see the manual)(by Hester).


v1.06.121108 

This version reads and writes positioning information for BrainVoyager project files (*.vmr/*.fmr/*.dmr). Keep on checking.
NIfTI-1 converter v1.06.121108 on Linux (SUSE 10.2)
Enlarge
NIfTI-1 converter v1.06.121108 on Linux (SUSE 10.2)

v1.05.220908 

This version writes rough positioning information for imported files. Please check thoroughly, in particular for flips.


v1.05.280808 

This version imports (statistical) maps. Also, *.dmr and *.fmr intensity values will be scaled in case of 
very high intensity values. The manual has been updated to v0.6. No positioning information.


matlab code

  • Matlab script to compute positioning information of a NIfTI file for VMR/FMR files. This writes a text file with positioning information. Change the positioning in BrainVoyager > 'File' > 'VMR Properties' > 'POS info...' button > 'Change...'. (Latest update: 15-06-09; now including the MeX files (see below) and document).
  • Experimental Matlab-MeX interface (v0.9) to read NIfTI-1 data, based on source code of R.W. Cox (NIH). Documentation is available in the chapter 'NIfTI-1 converter utilities for BrainVoyager QX' of the documentation for the plugin version 1.04 (see above). It might be that rows and columns are exchanged, you are warned; any comments, remarks, etc are welcome.


GIfTI

Introduction

GIfTI is a file format standard for by and for the neuroimaging community for anything related surface files. In BrainVoyager QX these are, among others, the mesh surface files (*.srf), mesh time courses (*.mtc) and statistical files (*.smp) (see the BrainVoyager QX file formats page for more information).

The GIfTI format has been developed by the GIfTI committee, which is supported by the NIH. Chair is Ziad Saad. The format is conveniently formulated in the eXtensible Markup Language (XML); XML is defined by the W3 consortium. XML gives the format flexibility, also to incorporate data from future developments in acquisition techniques. We are aiming to write GIfTI files from BrainVoyager QX before Human Brain Mapping 2008; reading at least before end of 2008. See also the project page at the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).


Documentation


Tools

Plugin versions

  • giftiplugin v0.1.270808

For exporting surfaces (*.srf), time series (*.mtc) and *.smp to GIfTI (*.gii) (see figure below). By Joost and Hester

Windows XP: For Windows XP Including plugin help. (Latest update: 29-August-08).
Mac OS 10.5 (Intel): For Mac OS 10.5 Including plugin help. (Latest update: 29-August-08).


  • giftiplugin v0.0

For exporting surfaces. Is ancient (was prototype) so is not compliant to current GIfTI format. It will, though, nicely export surface data to XML/DAT pairs. The header information is exported to an XML ascii file, the data are exported to a binary *.dat file.

It comes absolutely without any warranty, but anyone is free to export the surface files to this pre-prototype of the GIfTI (geometry-NIfTI) data format. It is using the nice TinyXML library (http://tinyxml.sourceforge.net/). And this little script to read exported data in Matlab (requires 'xmltree' program of Flandin) might be useful. Help files for the BrainVoyager GIfTI early prototype plugin.

Windows XP: giftiplugin v0.0 (Latest update: prehistory).


Coordinate systems

More information about the differences in coordinate systems can be found in the niftiplugin manual; an overview is already provided in the figure below.

Coordinate systems in BrainVoyager, NIfTI and DICOM


(by Hester)

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