Load NIFTI dataset body after its header is loaded using load_nii_hdr.
Usage: [img,hdr] = ...
load_nii_img_cbi(hdr,filetype,fileprefix,machine,[img_idx],[old_RGB]);
Where: [hdr,filetype,fileprefix,machine] = load_nii_hdr(filename);
img_idx - a numerical array of image indices. Only the specified images
will be loaded. If there is no img_idx, all images will be loaded. The
number of images scans can be obtained from hdr.dime.dim(5)
old_RGB - an optional boolean variable to handle special RGB data
sequence [R1 R2 ... G1 G2 ... B1 B2 ...] that is used only by
AnalyzeDirect (Analyze Software). Since both NIfTI and Analyze
file format use RGB triple [R1 G1 B1 R2 G2 B2 ...] sequentially
for each voxel, this variable is set to FALSE by default. If the
image that you displayed is garbled, try to set old_RGB variable
to TRUE (or 1) and load the image again, because it could be using
AnalyzeDirect RGB data sequence.
Returned values:
img - 3D (or 4D) matrix of NIFTI data.
Part of this file is copied and modified under GNU license from
MRI_TOOLBOX developed by CNSP in Flinders University, Australia
NIFTI data format can be found on: http://nifti.nimh.nih.gov
- Jimmy Shen (pls@rotman-baycrest.on.ca)0001 % Load NIFTI dataset body after its header is loaded using load_nii_hdr. 0002 % 0003 % Usage: [img,hdr] = ... 0004 % load_nii_img_cbi(hdr,filetype,fileprefix,machine,[img_idx],[old_RGB]); 0005 % 0006 % Where: [hdr,filetype,fileprefix,machine] = load_nii_hdr(filename); 0007 % 0008 % img_idx - a numerical array of image indices. Only the specified images 0009 % will be loaded. If there is no img_idx, all images will be loaded. The 0010 % number of images scans can be obtained from hdr.dime.dim(5) 0011 % 0012 % old_RGB - an optional boolean variable to handle special RGB data 0013 % sequence [R1 R2 ... G1 G2 ... B1 B2 ...] that is used only by 0014 % AnalyzeDirect (Analyze Software). Since both NIfTI and Analyze 0015 % file format use RGB triple [R1 G1 B1 R2 G2 B2 ...] sequentially 0016 % for each voxel, this variable is set to FALSE by default. If the 0017 % image that you displayed is garbled, try to set old_RGB variable 0018 % to TRUE (or 1) and load the image again, because it could be using 0019 % AnalyzeDirect RGB data sequence. 0020 % 0021 % Returned values: 0022 % 0023 % img - 3D (or 4D) matrix of NIFTI data. 0024 % 0025 % Part of this file is copied and modified under GNU license from 0026 % MRI_TOOLBOX developed by CNSP in Flinders University, Australia 0027 % 0028 % NIFTI data format can be found on: http://nifti.nimh.nih.gov 0029 % 0030 % - Jimmy Shen (pls@rotman-baycrest.on.ca) 0031 % 0032 function [img,hdr] = load_nii_img_cbi(hdr,filetype,fileprefix,machine,img_idx,old_RGB) 0033 0034 if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var') 0035 error('Usage: [img,hdr] = load_nii_img_cbi(hdr,filetype,fileprefix,machine,[img_idx]);'); 0036 end 0037 0038 if ~exist('img_idx','var') | hdr.dime.dim(5)<1, img_idx = []; end 0039 if ~exist('old_RGB','var'), old_RGB = 0; end 0040 0041 % check img_idx 0042 % 0043 if ~isempty(img_idx) & ~isnumeric(img_idx) 0044 error('"img_idx" should be a numerical array.'); 0045 end 0046 0047 if length(unique(img_idx)) ~= length(img_idx) 0048 error('Duplicate image index in "img_idx"'); 0049 end 0050 0051 if ~isempty(img_idx) & (min(img_idx) < 1 | max(img_idx) > hdr.dime.dim(5)) 0052 max_range = hdr.dime.dim(5); 0053 0054 if max_range == 1 0055 error(['"img_idx" should be 1.']); 0056 else 0057 range = ['1 ' num2str(max_range)]; 0058 error(['"img_idx" should be an integer within the range of [' range '].']); 0059 end 0060 end 0061 0062 [img,hdr] = read_image(hdr,filetype,fileprefix,machine,img_idx,old_RGB); 0063 0064 return % load_nii_img_cbi 0065 0066 0067 %--------------------------------------------------------------------- 0068 function [img,hdr] = read_image(hdr, filetype,fileprefix,machine,img_idx,old_RGB) 0069 0070 switch filetype 0071 case {0, 1} 0072 fn = [fileprefix '.img']; 0073 case 2 0074 fn = [fileprefix '.nii']; 0075 end 0076 0077 fid = fopen(fn,'r',machine); 0078 0079 if fid < 0, 0080 msg = sprintf('Cannot open file %s.',fn); 0081 error(msg); 0082 end 0083 0084 % Set bitpix according to datatype 0085 % 0086 % /*Acceptable values for datatype are*/ 0087 % 0088 % 0 None (Unknown bit per voxel) % DT_NONE, DT_UNKNOWN 0089 % 1 Binary (ubit1, bitpix=1) % DT_BINARY 0090 % 2 Unsigned char (uchar or uint8, bitpix=8) % DT_UINT8, NIFTI_TYPE_UINT8 0091 % 4 Signed short (int16, bitpix=16) % DT_INT16, NIFTI_TYPE_INT16 0092 % 8 Signed integer (int32, bitpix=32) % DT_INT32, NIFTI_TYPE_INT32 0093 % 16 Floating point (single or float32, bitpix=32) % DT_FLOAT32, NIFTI_TYPE_FLOAT32 0094 % 32 Complex, 2 float32 (Use float32, bitpix=64) % DT_COMPLEX64, NIFTI_TYPE_COMPLEX64 0095 % 64 Double precision (double or float64, bitpix=64) % DT_FLOAT64, NIFTI_TYPE_FLOAT64 0096 % 128 uint8 RGB (Use uint8, bitpix=24) % DT_RGB24, NIFTI_TYPE_RGB24 0097 % 256 Signed char (schar or int8, bitpix=8) % DT_INT8, NIFTI_TYPE_INT8 0098 % 511 Single RGB (Use float32, bitpix=96) % DT_RGB96, NIFTI_TYPE_RGB96 0099 % 512 Unsigned short (uint16, bitpix=16) % DT_UNINT16, NIFTI_TYPE_UNINT16 0100 % 768 Unsigned integer (uint32, bitpix=32) % DT_UNINT32, NIFTI_TYPE_UNINT32 0101 % 1024 Signed long long (int64, bitpix=64) % DT_INT64, NIFTI_TYPE_INT64 0102 % 1280 Unsigned long long (uint64, bitpix=64) % DT_UINT64, NIFTI_TYPE_UINT64 0103 % 1536 Long double, float128 (Unsupported, bitpix=128) % DT_FLOAT128, NIFTI_TYPE_FLOAT128 0104 % 1792 Complex128, 2 float64 (Use float64, bitpix=128) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128 0105 % 2048 Complex256, 2 float128 (Unsupported, bitpix=256) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128 0106 % 0107 switch hdr.dime.datatype 0108 case 1, 0109 hdr.dime.bitpix = 1; precision = 'ubit1'; 0110 case 2, 0111 hdr.dime.bitpix = 8; precision = 'uint8'; 0112 case 4, 0113 hdr.dime.bitpix = 16; precision = 'int16'; 0114 case 8, 0115 hdr.dime.bitpix = 32; precision = 'int32'; 0116 case 16, 0117 hdr.dime.bitpix = 32; precision = 'float32'; 0118 case 32, 0119 hdr.dime.bitpix = 64; precision = 'float32'; 0120 case 64, 0121 hdr.dime.bitpix = 64; precision = 'float64'; 0122 case 128, 0123 hdr.dime.bitpix = 24; precision = 'uint8'; 0124 case 256 0125 hdr.dime.bitpix = 8; precision = 'int8'; 0126 case 511 0127 hdr.dime.bitpix = 96; precision = 'float32'; 0128 case 512 0129 hdr.dime.bitpix = 16; precision = 'uint16'; 0130 case 768 0131 hdr.dime.bitpix = 32; precision = 'uint32'; 0132 case 1024 0133 hdr.dime.bitpix = 64; precision = 'int64'; 0134 case 1280 0135 hdr.dime.bitpix = 64; precision = 'uint64'; 0136 case 1792, 0137 hdr.dime.bitpix = 128; precision = 'float64'; 0138 otherwise 0139 error('This datatype is not supported'); 0140 end 0141 0142 if hdr.dime.dim(5) < 1 0143 hdr.dime.dim(5) = 1; 0144 end 0145 0146 % move pointer to the start of image block 0147 % 0148 switch filetype 0149 case {0, 1} 0150 fseek(fid, 0, 'bof'); 0151 case 2 0152 fseek(fid, hdr.dime.vox_offset, 'bof'); 0153 end 0154 0155 % Load whole image block for old Analyze format, or binary image, 0156 % or img_idx is empty; otherwise, load images that are specified 0157 % in img_idx 0158 % 0159 % For binary image, we have to read all because pos can not be 0160 % seeked in bit and can not be calculated the way below. 0161 % 0162 if filetype == 0 | hdr.dime.datatype == 1 | isempty(img_idx) 0163 0164 % For each frame, precision of value will be read 0165 % in img_siz times, where img_siz is only the 0166 % dimension size of an image, not the byte storage 0167 % size of an image. 0168 % 0169 img_siz = prod(hdr.dime.dim(2:5)); 0170 0171 % For complex float32 or complex float64, voxel values 0172 % include [real, imag] 0173 % 0174 if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792 0175 img_siz = img_siz * 2; 0176 end 0177 0178 %MPH: For RGB24, voxel values include 3 separate color planes 0179 % 0180 if hdr.dime.datatype == 128 | hdr.dime.datatype == 511 0181 img_siz = img_siz * 3; 0182 end 0183 0184 img = fread(fid, img_siz, sprintf('*%s',precision)); 0185 0186 else 0187 img = []; 0188 0189 for i=1:length(img_idx) 0190 0191 % For each frame, precision of value will be read 0192 % in img_siz times, where img_siz is only the 0193 % dimension size of an image, not the byte storage 0194 % size of an image. 0195 % 0196 img_siz = prod(hdr.dime.dim(2:4)); 0197 0198 % Position is seeked in bytes. To convert dimension size 0199 % to byte storage size, hdr.dime.bitpix/8 will be 0200 % applied. 0201 % 0202 % (MPH: This offset must be calculated BEFORE altering img_siz 0203 % for the datatypes for which 'bitpix' and 'precision' do not 0204 % "match"). 0205 % 0206 pos = (img_idx(i) - 1) * img_siz * hdr.dime.bitpix/8; 0207 0208 % For complex float32 or complex float64, voxel values 0209 % include [real, imag] 0210 % 0211 if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792 0212 img_siz = img_siz * 2; 0213 end 0214 0215 %MPH: For RGB24, voxel values include 3 separate color planes 0216 % 0217 if hdr.dime.datatype == 128 | hdr.dime.datatype == 511 0218 img_siz = img_siz * 3; 0219 end 0220 0221 if filetype == 2 0222 fseek(fid, pos + hdr.dime.vox_offset, 'bof'); 0223 else 0224 fseek(fid, pos, 'bof'); 0225 end 0226 0227 % For each frame, fread will read precision of value 0228 % in img_siz times 0229 % 0230 img = [img fread(fid, img_siz, sprintf('*%s',precision))]; 0231 end 0232 end 0233 0234 % For complex float32 or complex float64, voxel values 0235 % include [real, imag] 0236 % 0237 if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792 0238 img = reshape(img, [2, length(img)/2]); 0239 img = complex(img(1,:)', img(2,:)'); 0240 end 0241 0242 fclose(fid); 0243 0244 % Update the global min and max values 0245 % 0246 hdr.dime.glmax = max(double(img(:))); 0247 hdr.dime.glmin = min(double(img(:))); 0248 0249 if isempty(img_idx) 0250 img_idx = 1:hdr.dime.dim(5); 0251 end 0252 0253 if old_RGB & hdr.dime.datatype == 128 & hdr.dime.bitpix == 24 0254 img = squeeze(reshape(img, [hdr.dime.dim(2:3) 3 hdr.dime.dim(4) length(img_idx)])); 0255 img = permute(img, [1 2 4 3 5]); 0256 elseif hdr.dime.datatype == 128 & hdr.dime.bitpix == 24 0257 img = squeeze(reshape(img, [3 hdr.dime.dim(2:4) length(img_idx)])); 0258 img = permute(img, [2 3 4 1 5]); 0259 elseif hdr.dime.datatype == 511 & hdr.dime.bitpix == 96 0260 img = double(img); 0261 img = (img - min(img))/(max(img) - min(img)); 0262 img = squeeze(reshape(img, [3 hdr.dime.dim(2:4) length(img_idx)])); 0263 img = permute(img, [2 3 4 1 5]); 0264 else 0265 img = squeeze(reshape(img, [hdr.dime.dim(2:4) length(img_idx)])); 0266 end 0267 0268 if ~isempty(img_idx) 0269 hdr.dime.dim(5) = length(img_idx); 0270 end 0271 0272 return % read_image 0273