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NIfTI conversion (volumetric files)

Available Tools - Available Plugins
PDF 

Description of the NIfTI converter plugin:

NIfTI is a data format to save volumetric (f)MRI data and is the successor of Analyze 7.5. A NIfTI file consists of header and image data, saved in one *.nii file or a *.hdr and an *.img file (for more information, see http://nifti.nimh.nih.gov/ and http://www.nitrc.org/projects/nifti).

Conversions of the following files are possible:

  • BrainVoyager Volumetric MR (*.vmr)
  • BrainVoyager Functional MR (*.fmr)
  • BrainVoyager Volume Time Course (*.vtc)
  • BrainVoyager Diffusion (weighted) MR (*.dmr)
  • BrainVoyager Volume (statistical output) Map (*.vmp)
  • BrainVoyager Volume of Interest (*.voi)
  • NIFTI (*.nii or *.hdr+*.img)
  • For conversion of surface data (*.srf, *.mtc, *.smp, *.poi), see the GIFTI plugin.
News (10-01-2012): Revision process for NIfTI converter plugin due to reported alignment issues. In the next period the plugin will be revised according to the six stages specified below.
1. Review theoretical basis for conversion (current stage)
2. Test of corrected theoretical basis with scripts
3. Update NIfTI converter design document (design available on request)
4. Update NIfTI converter, check import and export of each format
5. Implement preservation of positioning information for import and export of subvolume images (VMP, VTC)
6. Remaining issues

Latest versions of the plugin:

Version 1.09.021111: better memory management, improved positioning for export AR-VMP (when using options: TAL space, 1mm3, zeropad).
Compilations: Mac OS X, Windows 32-bit, Windows 64-bit, Linux 64-bit (not tested).

Version 1.08.220811: update version containing possibilities to copy the NIfTI header to another NIfTI file, and to manipulate positioning header fields. (For documentation of the header fields, see http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields.) Also, the transformation matrix for export of VMR has been changed, which will be used when the 'transform' and 'reset orient' flags are checked. Compilations: Mac OS X (other operating systems and updated manual to follow); latest update 19-09-11 (fix 4th column in srow matrix of Change header tab), Windows 32-bit,

nifticonverter_v108220811_changeheadertab

Version 1.08.040511: small update version (added zero-padding for VMPs at import, which makes reorienting the volume at import possible) available: for Mac OS X (32 and 64 bit), for Windows (32-bit) and (64-bit). 

Version 1.08.180610: new user interface and image transformation module: for Mac OS X (32 and 64 bit), for Windows (32-bit), Windows (64-bit) and Linux  (32-bit), Linux (64-bit).

* Manual for version 1.08.180610: PDF.

nifticonverter_gui_v1.08.180610_bvqx21_macosx

Other tools and information:

* Addendum for image transformations module (transformations sheet): PDF (v1).

* Matlab script bundle to fix position information in NIfTI files imported in BrainVoyager files for coregistration: nifti2brainvoyager bundle. Usage: set current path in Matlab to unzipped script bundle directory, open and run the nifti2brainvoyager.m script. For Windows. For further use, see included PDF.

*  Matlab script to compute position information in NIfTI coordinates from an FMR: fmrpos2nifti.zip. This script uses BVQXtools by Jochen Weber to read the FMR.

*  Matlab script to compare the first volume of a BrainVoyager and NIfTI-1 functional dataset: compare_brainvoyager_nifti_datasets.zip. Usage: invoke from command line via compare_brainvoyager_nifti_datasets(dimx, dimy, dimz, dimt, topic). Two file dialogs will appear, the first to select an *.fmr file, the second for a NIfTI-1 file. Five comparative figures will be produced (histogram, difference image, etc).

* Matlab tools to manipulate Nifti images

 

Older versions of the plugin:

A preview of the plugin to convert between NIfTI and BrainVoyager formats in BrainVoyager QX 2.1 with user interface:
* Preview version of plugin v1.07.010410 for Mac OS 10.6 (most functions are enabled), 64-bit. Converter v1.07.190410 for 32 and 64 bit on Mac OS 10.5 an 10.6 (finalised zero-padding for export of VMPs).
* Preview version of plugin v1.07.010410 for Windows 7 (most functions are enabled), 32-bit. Converter v1.07.190410 for Windows 32 bit (finalised zero-padding for export of VMPs).
* Manual for preview version: PDF 

A plugin (v1.07.091209) to convert between NIfTI and BrainVoyager formats in BrainVoyager QX 2.1 can be found below:

* Plugin for Windows Vista (unstable plugin version)
* Plugin for Windows 7 32-bit (stable plugin version): v1.07.091209, v1.07.050210
* Plugin for Mac OS 10.6 64-bit (stable plugin versions): v1.07.091209, v1.07.050210
* Plugin for Linux Kubuntu 9.10, 32-bit (stable plugin versions): v1.07.091209, v1.07.050210 (with DMR import fix)

The plugins (v1.07.091209) to convert between NIfTI and BrainVoyager formats in BrainVoyager QX 2.0 can be found below:

* Plugin for Windows XP
* Plugin for Mac OS 10.5 (Intel)
* Plugin for Mac OS 10.5 (Intel) and Windows XP where import VMP is more or less fixed (02-12-09) (is quick fix, other functions have not been re-tested).
* NIfTI converter manual (v0.8)

Figure: exported VOI in FSLView and BrainVoyager

VOIinFSLviewandBVQX

 

Changes w.r.t. to the previous version:

- import VMP problem fixed (quick fix)(Windows XP/Mac OS X, 02-12-09)
- more float adaptations for DMR, FMR, VTC (Windows XP, 10-09-09)
- bug in export to VTCs fixed (temporary version, Windows XP/Mac OS X, 27-08-09)
- FMR’s STC files are written in float format
- the converter asks whether to reorient images and rescale intensity values rather than just doing it
- the positioning conversion procedure for import of VMR and FMR was broken (again) and fixed (again)
- for importing anatomical volumes also *.v16 images are written
- if the anatomical volume is reoriented during conversion, this is saved in the “past transformations” header

If you skipped a version:
- VOI files can now be exported

 

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