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niiformat.m
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niiformat.m
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function niiheader = niiformat(format)
%
% niiheader=niiformat(format)
%
% Return a NIfTI header format descriptor as an Nx3 cell array
%
% author: Qianqian Fang (q.fang <at> neu.edu)
%
% input:
% format:'nifti1' - return the header descriptor for NIfTI-1 format
% 'nifti2' - return the header descriptor for NIfTI-2 format
%
% output:
% niiheader: an Nx3 cell array in the format similar to the 'Format'
% specifier of the memmapfile.m function in MATLAB
% It has the following structure:
%
% column 1: data type string, it can be one of the following
% 'int8','int16','int32','int64',
% 'uint8','uint16','uint32','uint64',
% 'single','double'
% column 2: an integer vector denoting the size of the data
% column 3: a string denoting the fieldname in the output struct
%
% this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifti
%
% License: Apache 2.0, see https://github.com/NeuroJSON/jnifti for details
%
header.nifti1 = { ...
'int32' [1 1] 'sizeof_hdr' % !< MUST be 348 % % int sizeof_hdr; % ...
'int8' [1 10] 'data_type' % !< ++UNUSED++ % % char data_type[10]; % ...
'int8' [1 18] 'db_name' % !< ++UNUSED++ % % char db_name[18]; % ...
'int32' [1 1] 'extents' % !< ++UNUSED++ % % int extents; % ...
'int16' [1 1] 'session_error' % !< ++UNUSED++ % % short session_error; % ...
'int8' [1 1] 'regular' % !< ++UNUSED++ % % char regular; % ...
'int8' [1 1] 'dim_info' % !< MRI slice ordering. % % char hkey_un0; % ...
'uint16' [1 8] 'dim' % !< Data array dimensions.% % short dim[8]; % ...
'single' [1 1] 'intent_p1' % !< 1st intent parameter. % % short unused8/9; % ...
'single' [1 1] 'intent_p2' % !< 2nd intent parameter. % % short unused10/11; % ...
'single' [1 1] 'intent_p3' % !< 3rd intent parameter. % % short unused12/13; % ...
'int16' [1 1] 'intent_code' % !< NIFTI_INTENT_* code. % % short unused14; % ...
'int16' [1 1] 'datatype' % !< Defines data type! % % short datatype; % ...
'int16' [1 1] 'bitpix' % !< Number bits/voxel. % % short bitpix; % ...
'int16' [1 1] 'slice_start' % !< First slice index. % % short dim_un0; % ...
'single' [1 8] 'pixdim' % !< Grid spacings. % % float pixdim[8]; % ...
'single' [1 1] 'vox_offset' % !< Offset into .nii file % % float vox_offset; % ...
'single' [1 1] 'scl_slope' % !< Data scaling: slope. % % float funused1; % ...
'single' [1 1] 'scl_inter' % !< Data scaling: offset. % % float funused2; % ...
'int16' [1 1] 'slice_end' % !< Last slice index. % % float funused3; % ...
'int8' [1 1] 'slice_code' % !< Slice timing order. % ...
'int8' [1 1] 'xyzt_units' % !< Units of pixdim[1..4] % ...
'single' [1 1] 'cal_max' % !< Max display intensity % % float cal_max; % ...
'single' [1 1] 'cal_min' % !< Min display intensity % % float cal_min; % ...
'single' [1 1] 'slice_duration' % !< Time for 1 slice. % % float compressed; % ...
'single' [1 1] 'toffset' % !< Time axis shift. % % float verified; % ...
'int32' [1 1] 'glmax' % !< ++UNUSED++ % % int glmax; % ...
'int32' [1 1] 'glmin' % !< ++UNUSED++ % % int glmin; % ...
'int8' [1 80] 'descrip' % !< any text you like. % % char descrip[80]; % ...
'int8' [1 24] 'aux_file' % !< auxiliary filename. % % char aux_file[24]; % ...
'int16' [1 1] 'qform_code' % !< NIFTI_XFORM_* code. % %-- all ANALYZE 7.5 --- % ...
'int16' [1 1] 'sform_code' % !< NIFTI_XFORM_* code. % %below here are replaced% ...
'single' [1 1] 'quatern_b' % !< Quaternion b param. % ...
'single' [1 1] 'quatern_c' % !< Quaternion c param. % ...
'single' [1 1] 'quatern_d' % !< Quaternion d param. % ...
'single' [1 1] 'qoffset_x' % !< Quaternion x shift. % ...
'single' [1 1] 'qoffset_y' % !< Quaternion y shift. % ...
'single' [1 1] 'qoffset_z' % !< Quaternion z shift. % ...
'single' [1 4] 'srow_x' % !< 1st row affine transform. % ...
'single' [1 4] 'srow_y' % !< 2nd row affine transform. % ...
'single' [1 4] 'srow_z' % !< 3rd row affine transform. % ...
'int8' [1 16] 'intent_name' % !< 'name' or meaning of data. % ...
'int8' [1 4] 'magic' % !< MUST be "ni1\0" or "n+1\0". % ...
'int8' [1 4] 'extension' % !< header extension % ...
};
header.nifti2 = { ...
'int32' [1 1] 'sizeof_hdr' % !< MUST be 540 % % int sizeof_hdr; % ...
'int8' [1 8] 'magic' % !< MUST be "ni2\0" or "n+2\0". % ...
'int16' [1 1] 'datatype' % !< Defines data type! % % short datatype; % ...
'int16' [1 1] 'bitpix' % !< Number bits/voxel. % % short bitpix; % ...
'int64' [1 8] 'dim' % !< Data array dimensions.% % short dim[8]; % ...
'double' [1 1] 'intent_p1' % !< 1st intent parameter. % % short unused8/9; % ...
'double' [1 1] 'intent_p2' % !< 2nd intent parameter. % % short unused10/11; % ...
'double' [1 1] 'intent_p3' % !< 3rd intent parameter. % % short unused12/13; % ...
'double' [1 8] 'pixdim' % !< Grid spacings. % % float pixdim[8]; % ...
'int64' [1 1] 'vox_offset' % !< Offset into .nii file % % float vox_offset; % ...
'double' [1 1] 'scl_slope' % !< Data scaling: slope. % % float funused1; % ...
'double' [1 1] 'scl_inter' % !< Data scaling: offset. % % float funused2; % ...
'double' [1 1] 'cal_max' % !< Max display intensity % % float cal_max; % ...
'double' [1 1] 'cal_min' % !< Min display intensity % % float cal_min; % ...
'double' [1 1] 'slice_duration' % !< Time for 1 slice. % % float compressed; % ...
'double' [1 1] 'toffset' % !< Time axis shift. % % float verified; % ...
'int64' [1 1] 'slice_start' % !< First slice index. % % short dim_un0; % ...
'int64' [1 1] 'slice_end' % !< Last slice index. % % float funused3; % ...
'int8' [1 80] 'descrip' % !< any text you like. % % char descrip[80]; % ...
'int8' [1 24] 'aux_file' % !< auxiliary filename. % % char aux_file[24]; % ...
'int32' [1 1] 'qform_code' % !< NIFTI_XFORM_* code. % %-- all ANALYZE 7.5 --- % ...
'int32' [1 1] 'sform_code' % !< NIFTI_XFORM_* code. % %below here are replaced% ...
'double' [1 1] 'quatern_b' % !< Quaternion b param. % ...
'double' [1 1] 'quatern_c' % !< Quaternion c param. % ...
'double' [1 1] 'quatern_d' % !< Quaternion d param. % ...
'double' [1 1] 'qoffset_x' % !< Quaternion x shift. % ...
'double' [1 1] 'qoffset_y' % !< Quaternion y shift. % ...
'double' [1 1] 'qoffset_z' % !< Quaternion z shift. % ...
'double' [1 4] 'srow_x' % !< 1st row affine transform. % ...
'double' [1 4] 'srow_y' % !< 2nd row affine transform. % ...
'double' [1 4] 'srow_z' % !< 3rd row affine transform. % ...
'int32' [1 1] 'slice_code' % !< Slice timing order. % ...
'int32' [1 1] 'xyzt_units' % !< Units of pixdim[1..4] % ...
'int32' [1 1] 'intent_code' % !< NIFTI_INTENT_* code. % % short unused14; % ...
'int8' [1 16] 'intent_name' % !< 'name' or meaning of data. % ...
'int8' [1 1] 'dim_info' % !< MRI slice ordering. % % char hkey_un0; % ...
'int8' [1 15] 'reserved' % !< unused buffer % ...
'int8' [1 4] 'extension' % !< header extension % ...
};
if (nargin < 1)
format = 'nifti1';
end
format = lower(format);
if (isfield(header, format))
niiheader = header.(format);
else
error('format must be either nifti1 or nifti2');
end