NIfTI-1 image format

A variant (subset) of NIfTI-1 image format is supported in TPC. Most of the image processing and analysis programs are able to read and write this format, including Carimas and MAGIA pipeline.

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.

The Brain Imaging Data Structure (BIDS) could be an efficient way of storing and organizing PET data (Gorgolewski et al., 2016; Knudsen et al., 2020), especially in case of brain activation studies where several tasks are performed during one PET scan. PET-BIDS extension (Norgaard et al., 2022) is not yet supported by Carimas or TPCCLIB software, but it will the main image format of MAGIA pipeline.

Converting image file formats

Program ImageConverter is available for converting image data between NIfTI and other formats, including DICOM. ImageConverter can optionally create the SIF. In TPC, ImageConverter can be started from S:\petsoftware\bin\windows\ImageConverter.exe, elsewhere it can be downloaded from here.

Command-line tools

By default, ImageConverter opens a GUI, but it can also be used in Windows command prompt, which is faster when many image sets need to be converted. Enter command ImageConverter --help to get usage information, and see examples for converting multiple DICOM images to NIfTI.

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


See also:


Literature

NIFTI documentation. http://nifti.nimh.nih.gov/nifti-1/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.

Norgaard et al. PET-BIDS, an extension to the brain imaging data structure for positron emission tomography. Sci Data 2022; 9:65. doi: 10.1038/s41597-022-01164-1.



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Updated at: 2023-12-12
Created at: 2013-05-07
Written by: Vesa Oikonen