/
extra_nii_hdr.m
255 lines (236 loc) · 7.9 KB
/
extra_nii_hdr.m
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% Decode extra NIFTI header information into hdr.extra
%
% Usage: hdr = extra_nii_hdr(hdr)
%
% hdr can be obtained from load_nii_hdr
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function hdr = extra_nii_hdr(hdr)
switch hdr.dime.datatype
case 1
extra.NIFTI_DATATYPES = 'DT_BINARY';
case 2
extra.NIFTI_DATATYPES = 'DT_UINT8';
case 4
extra.NIFTI_DATATYPES = 'DT_INT16';
case 8
extra.NIFTI_DATATYPES = 'DT_INT32';
case 16
extra.NIFTI_DATATYPES = 'DT_FLOAT32';
case 32
extra.NIFTI_DATATYPES = 'DT_COMPLEX64';
case 64
extra.NIFTI_DATATYPES = 'DT_FLOAT64';
case 128
extra.NIFTI_DATATYPES = 'DT_RGB24';
case 256
extra.NIFTI_DATATYPES = 'DT_INT8';
case 512
extra.NIFTI_DATATYPES = 'DT_UINT16';
case 768
extra.NIFTI_DATATYPES = 'DT_UINT32';
case 1024
extra.NIFTI_DATATYPES = 'DT_INT64';
case 1280
extra.NIFTI_DATATYPES = 'DT_UINT64';
case 1536
extra.NIFTI_DATATYPES = 'DT_FLOAT128';
case 1792
extra.NIFTI_DATATYPES = 'DT_COMPLEX128';
case 2048
extra.NIFTI_DATATYPES = 'DT_COMPLEX256';
otherwise
extra.NIFTI_DATATYPES = 'DT_UNKNOWN';
end
switch hdr.dime.intent_code
case 2
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CORREL';
case 3
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TTEST';
case 4
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_FTEST';
case 5
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_ZSCORE';
case 6
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHISQ';
case 7
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_BETA';
case 8
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_BINOM';
case 9
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_GAMMA';
case 10
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_POISSON';
case 11
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NORMAL';
case 12
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_FTEST_NONC';
case 13
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHISQ_NONC';
case 14
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOGISTIC';
case 15
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LAPLACE';
case 16
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_UNIFORM';
case 17
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TTEST_NONC';
case 18
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_WEIBULL';
case 19
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHI';
case 20
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_INVGAUSS';
case 21
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_EXTVAL';
case 22
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_PVAL';
case 23
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOGPVAL';
case 24
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOG10PVAL';
case 1001
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_ESTIMATE';
case 1002
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LABEL';
case 1003
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NEURONAME';
case 1004
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_GENMATRIX';
case 1005
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_SYMMATRIX';
case 1006
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_DISPVECT';
case 1007
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_VECTOR';
case 1008
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_POINTSET';
case 1009
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TRIANGLE';
case 1010
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_QUATERNION';
case 1011
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_DIMLESS';
otherwise
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NONE';
end
extra.NIFTI_INTENT_NAMES = hdr.hist.intent_name;
if hdr.hist.sform_code > 0
switch hdr.hist.sform_code
case 1
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_SCANNER_ANAT';
case 2
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_ALIGNED_ANAT';
case 3
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_TALAIRACH';
case 4
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_MNI_152';
otherwise
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
end
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
elseif hdr.hist.qform_code > 0
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
switch hdr.hist.qform_code
case 1
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_SCANNER_ANAT';
case 2
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_ALIGNED_ANAT';
case 3
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_TALAIRACH';
case 4
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_MNI_152';
otherwise
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
end
else
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
end
switch bitand(hdr.dime.xyzt_units, 7) % mask with 0x07
case 1
extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_METER';
case 2
extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_MM'; % millimeter
case 3
extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_MICRO';
otherwise
extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_UNKNOWN';
end
switch bitand(hdr.dime.xyzt_units, 56) % mask with 0x38
case 8
extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_SEC';
case 16
extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_MSEC';
case 24
extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_USEC'; % microsecond
otherwise
extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_UNKNOWN';
end
switch hdr.dime.xyzt_units
case 32
extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_HZ';
case 40
extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_PPM'; % part per million
case 48
extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_RADS'; % radians per second
otherwise
extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_UNKNOWN';
end
% MRI-specific spatial and temporal information
%
dim_info = hdr.hk.dim_info;
extra.NIFTI_FREQ_DIM = bitand(dim_info, 3);
extra.NIFTI_PHASE_DIM = bitand(bitshift(dim_info, -2), 3);
extra.NIFTI_SLICE_DIM = bitand(bitshift(dim_info, -4), 3);
% Check slice code
%
switch hdr.dime.slice_code
case 1
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_SEQ_INC'; % sequential increasing
case 2
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_SEQ_DEC'; % sequential decreasing
case 3
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_INC'; % alternating increasing
case 4
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_DEC'; % alternating decreasing
case 5
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_INC2'; % ALT_INC # 2
case 6
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_DEC2'; % ALT_DEC # 2
otherwise
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_UNKNOWN';
end
% Check NIFTI version
%
if ~isempty(hdr.hist.magic) & strcmp(hdr.hist.magic(1),'n') & ...
( strcmp(hdr.hist.magic(2),'i') | strcmp(hdr.hist.magic(2),'+') ) & ...
str2num(hdr.hist.magic(3)) >= 1 & str2num(hdr.hist.magic(3)) <= 9
extra.NIFTI_VERSION = str2num(hdr.hist.magic(3));
else
extra.NIFTI_VERSION = 0;
end
% Check if data stored in the same file (*.nii) or separate
% files (*.hdr/*.img)
%
if isempty(hdr.hist.magic)
extra.NIFTI_ONEFILE = 0;
else
extra.NIFTI_ONEFILE = strcmp(hdr.hist.magic(2), '+');
end
% Swap has been taken care of by checking whether sizeof_hdr is
% 348 (machine is 'ieee-le' or 'ieee-be' etc)
%
% extra.NIFTI_NEEDS_SWAP = (hdr.dime.dim(1) < 0 | hdr.dime.dim(1) > 7);
% Check NIFTI header struct contains a 5th (vector) dimension
%
if hdr.dime.dim(1) > 4 & hdr.dime.dim(6) > 1
extra.NIFTI_5TH_DIM = hdr.dime.dim(6);
else
extra.NIFTI_5TH_DIM = 0;
end
hdr.extra = extra;
return; % extra_nii_hdr