function nii = mcxloadnii(filename) % % nii=mcxloadnii(filename) % % author: Qianqian Fang (q.fang neu.edu) % % input: % fname: the file name to the .nii file % % output: % nii.img: the data volume read from the nii file % nii.datatype: the data type of the voxel, in matlab data type string % nii.datalen: data count per voxel - for example RGB data has 3x % uint8 per voxel, so datatype='uint8', datalen=3 % nii.voxelbyte: total number of bytes per voxel: for RGB data, % voxelbyte=3; also voxelbyte=header.bitpix/8 % nii.hdr: file header info, a structure has the full nii header % key subfileds include % % sizeof_hdr: must be 348 % dim: short array, dim(2: dim(1)+1) defines the array size % datatype: the type of data stored in each voxel % bitpix: total bits per voxel % magic: must be 'ni1\0' or 'n+1\0' % % For the detailed nii header, please see % https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h % % this file is part of Monte Carlo eXtreme (MCX) % License: GPLv3, see http://mcx.sf.net for details % header = memmapfile(filename, ... 'Offset', 0, ... 'Writable', false, ... 'Format', { ... '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 % ... }); nii.hdr = header.Data(1); type2byte = [ 0 0 % unknown % 1 0 % binary (1 bit/voxel) % 2 1 % unsigned char (8 bits/voxel) % 4 2 % signed short (16 bits/voxel) % 8 4 % signed int (32 bits/voxel) % 16 4 % float (32 bits/voxel) % 32 8 % complex (64 bits/voxel) % 64 8 % double (64 bits/voxel) % 128 3 % RGB triple (24 bits/voxel) % 255 0 % not very useful (?) % 256 1 % signed char (8 bits) % 512 2 % unsigned short (16 bits) % 768 4 % unsigned int (32 bits) % 1024 8 % long long (64 bits) % 1280 8 % unsigned long long (64 bits) % 1536 16 % long double (128 bits) % 1792 16 % double pair (128 bits) % 2048 32 % long double pair (256 bits) % 2304 4 % 4 byte RGBA (32 bits/voxel) % ]; type2str = { 'uint8' 0 % unknown % 'uint8' 0 % binary (1 bit/voxel) % 'uint8' 1 % unsigned char (8 bits/voxel) % 'uint16' 1 % signed short (16 bits/voxel) % 'int32' 1 % signed int (32 bits/voxel) % 'float32' 1 % float (32 bits/voxel) % 'float32' 2 % complex (64 bits/voxel) % 'float64' 1 % double (64 bits/voxel) % 'uint8' 3 % RGB triple (24 bits/voxel) % 'uint8' 0 % not very useful (?) % 'int8' 1 % signed char (8 bits) % 'uint16' 1 % unsigned short (16 bits) % 'uint32' 1 % unsigned int (32 bits) % 'long' 1 % long long (64 bits) % 'ulong' 1 % unsigned long long (64 bits) % 'uint8' 16 % long double (128 bits) % 'uint8' 16 % double pair (128 bits) % 'uint8' 32 % long double pair (256 bits) % 'uint8' 4 % 4 byte RGBA (32 bits/voxel) % }; typeidx = find(type2byte(:, 1) == nii.hdr.datatype); nii.datatype = type2str{typeidx, 1}; nii.datalen = type2str{typeidx, 2}; nii.voxelbyte = type2byte(typeidx, 2); if (type2byte(typeidx, 2) == 0) nii.img = []; return end if (type2str{typeidx, 2} > 1) nii.hdr.dim = [nii.hdr.dim(1) + 1 uint16(nii.datalen) nii.hdr.dim(2:end)]; end fid = fopen(filename, 'rb'); fseek(fid, nii.hdr.vox_offset, 'bof'); nii.img = fread(fid, prod(nii.hdr.dim(2:nii.hdr.dim(1) + 1)), [nii.datatype '=>' nii.datatype]); fclose(fid); nii.img = reshape(nii.img, nii.hdr.dim(2:nii.hdr.dim(1) + 1));