FYI _* _* _* _* _*A 64-bit update to the NIfTI format*_ *_ *_ *_ *_
The NIfTI committee are proposing the creation of a NIfTI-2 format that is a very simple extension of the current NIfTI-1 format, but updated to allow 64-bit storage and addressing for large images and matrices. _ _ It is intended that this format: - will enable the storage of large images and matrices, with all dimensions being coded by 64-bit integers rather than the current limitation of 16-bit signed integers (which currently gives a restrictive 32767 size limit in each dimension) - will be very simple to implement and update software (a couple of hours coding or less generally) - contains the same information as a NIfTI-1 file (no new fields and all current fields still retained) - will support the existing file formats and naming: a .nii single-file, a .hdr/.img file-pair and their gzipped versions - has a very simple test (see below) to determine if the file is NIfTI-1 or NIfTI-2 - does not replace NIfTI-1 in the short term but is supported alongside it *_Comments_* This announcement is intended for public comment. Please post any comments on this NIfTI-2 proposal to the NITRC discussion list (www.nitrc.org/forum/forum.php?forum_id=1941 <http://www.nitrc.org/forum/forum.php?forum_id=1941>) We ask that comments relating to larger-scale changes and requests for other types of format change be posted instead to a separate NITRC discussion list for more advanced neuroimaging formats (www.nitrc.org/forum/forum.php?forum_id=1942 <http://www.nitrc.org/forum/forum.php?forum_id=1942>) _* *_ _*Supporting software*_ - AFNI, BrainVoyager, Caret, Fiswidgets, FreeSurfer, FSL, ITK, LONI-DIRAC, MRIcron, NiBabel and SPM have all agreed to support the NIfTI-2 version in their upcoming releases, but that NIfTI-1 will remain a default output, or a configurable default, in the short-term - the sourceforge supporting libraries in niftilib will be updated so that they seemlessly support both NIfTI-1 and NIfTI-2 - conversion utilities to and from NIfTI-1 will be made available via sourceforge as well as in some of the software packages mentioned above _*Changes to the header *_The changes to the NIfTI header structure are the following: - short dim[8] becomes int64_t dim[8] - float intent_p1 becomes double intent_p1 - float intent_p2 becomes double intent_p2 - float intent_p3 becomes double intent_p3 - float pixdim[8] becomes double pixdim[8] - float vox_offset becomes int64_t vox_offset - float scl_slope becomes double scl_slope - float scl_inter becomes double scl_inter - float cal_max becomes double cal_max - float cal_min becomes double cal_min - float slice_duration becomes double slice_duration - float toffset becomes double toffset - float quatern_b becomes double quatern_b and similarly for quatern_c, quatern_d, qoffset_x, qoffset_y, qoffset_z - float srow_x[4] becomes double srow_x[4] and similarly for srow_y[4], srow_z[4] - char magic[4] becomes char magic[8] - char unused_str[12] is added after char magic[8] The order, size and type of all other fields remains unchanged. The sizeof_hdr must store 556 for a NIfTI-2 file instead of 348 for NIfTI-1. Extension information is still held in the first 4 bytes after this header (bytes 557-560) in the same way as in NIfTI-1. Note that the total block size of 560 (header + 4 bytes) retains the 16-byte alignment in NIfTI-1 (348+4=352), as needed for convenient memory-mapping. The changes of float to double are generally made to allow for more accurate mapping of intensities or indices when dealing with very large arrays, and unused_str is added to ensure the 16-byte alignment holds. _*Compatibility*_ This format is not, and cannot be, bit-wise compatible with the previous NIfTI-1 (or ANALYZE) formats and so will not work with existing NIfTI-1 software directly. In the short term this can be solved via conversion utilities. A NIfTI-2 image will not be recognised as a valid NIfTI-1 image by existing software and so no incorrect processing or analyses should occur. In the longer term most code should be very easily converted to work with both NIfTI-2 and NIfTI-1 by using the updated sourceforge libraries or making equivalent changes internally. The change in format is intentionally very minimal and should be very easy to code. *_Determining the NIfTI version_* The following pseudo-code shows how a file can be tested to see: (a) if it is a NIfTI image file, (b) what version of NIfTI it is, and (c) whether byte-swapping is required. read in the first 4 bytes from the file let d = the content of these bytes, formatted as a 32-bit int if (d==348) then it is a NIfTI-1 file, no byte-swapping required else if (swap_4bytes(d)==348) then it is a NIfTI-1 file, but with byte-swapping required else if (d==556) then it is a NIfTI-2 file, no byte-swapping required else if (swap_4bytes(d)==556) then it is a NIfTI-2 file, but with byte-swapping required else it is not a valid NIfTI file if it passed the above then read in the remaining 344 or 552 bytes of the header into the appropriate NIfTI-1 or NIfTI-2 struct double-check this is truly a valid NIfTI file by looking at dim[0] (should be between 0 and 7) and magic[] which should contain "ni1" or "n+1" followed by \0 for NIfTI-1, and "ni2" or "n+2" followed by \0 and 4 extra signature bytes for NIfTI-2 *_Magic Signature_* The magic string is expanded to 8 bytes with the first 4 bytes containing ones of the strings "ni2" or "n+2", terminated with \0. The next four bytes form a magic signature much the same as used by the PNG format (http://www.libpng.org/pub/png/pngintro.html), to detect for file transfer errors involving newline characters. The extra four bytes are the same as the last four in the PNG format - that is: |\r| |\n| |\032| |\n (||0D| |0A| |1A| |0A|) The magic string will have a different offset from the start of the file in NIfTI-1 and NIfTI-2 (344 and 536 bytes respectively). *_Timeline_* Barring any unknown unknowns or unforseeable unforseen problems, it is intended to begin rolling out this format in practice in March-April 2011. Example datasets will also be provided soon. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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