NIfTI-1 image format

A variant (subset) of NIfTI-1 image format is supported in TPC. Many of the image processing and analysis programs are able to read and write this format.

NIfTI image can be in single or dual file format: in the single file format (1S) both the header contents and image pixel data are stored in one .nii file, and in the dual file format (1D) the image pixel data is stored in .img file, and header contents in .hdr file. Note that Analyze 7.5 and Interfile images are stored with similar names than NIfTI dual file format.

NIfTI files do not contain time information (PET frames). Therefore, corresponding SIF data should always be kept with dynamic NIfTI images.

BIDS could be an efficient way of storing and organizing data (Gorgolewski et al., 2016); BIDS extension proposals for PET (BEP009 and BEP023) are under development, but not yet supported by TPC software.

Converting image file formats

Program ImageConverter (contact Timo Laitinen) is available for converting image data between NIfTI and other formats, including DICOM. ImageConverter can optionally create SIF. In TPC, ImageConverter can be started from P:\bin\windows\ImageConverter.exe, elsewhere it can be downloaded from here.

Command-line tools

Additionally, ECAT 6.3 images and ECAT 7 image volumes can be converted to NIfTI images using program ecat2nii, and NIfTI images can be converted to ECAT 6.3 images or ECAT 7 image volumes using nii2ecat. Ecat2nii can create SIF if option -sif is used.

Editing NIfTI-1 image headers


NIFTI documentation.

Cox RW, Ashburner J, Breman H, Fissell K, Haselgrove C, Holmes CJ, Lancaster JL, Rex DE, Smith SM, Woodward JB, Strother SC. A (sort of) new image data format standard: NIfTI-1. 10th Annual Meeting of the Organization for Human Brain Mapping, 2004.

Fischl B. FreeSurfer. Neuroimage 2012; 62(2): 774-781. doi: 10.1016/j.neuroimage.2012.01.021.

Gorgolewski KJ, Auer T, Calhoun VD, Craddock RC, Das S, Duff EP, Flandin G, Ghosh SS, Glatard T, Halchenko YO, Handwerker DA, Hanke M, Keator D, Li X, Michael Z, Maumet C, Nichols BN, Nichols TE, Pellman J, Poline J-B, Rokem A, Schaefer G, Sochat V, Triplett W, Turner JA, Varoquaux G, Poldrack RA. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Sci Data 2016; 3, 160044. doi: 10.1038/sdata.2016.44.

Li X, Morgan PS, Ashburner J, Smith J, Rorden C. The first step for neuroimaging data analysis: DICOM to NIfTI conversion. J Neurosci Methods 2016; 264: 47-56. doi: 10.1016/j.jneumeth.2016.03.001.

Muschelli J, Sweeney E, Crainiceanu CM. freesurfer: Connecting the Freesurfer software with R. F1000Res. 2018; 7:599. doi: 10.12688/f1000research.14361.1.

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Created at: 2013-05-07
Updated at: 2018-11-19
Written by: Vesa Oikonen