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Scheduled service maintenance on November 22

On Friday, November 22, 2024, between 06:00 CET and 18:00 CET, GIN services will undergo planned maintenance. Extended service interruptions should be expected. We will try to keep downtimes to a minimum, but recommend that users avoid critical tasks, large data uploads, or DOI requests during this time.

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NHP-pRF
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extra_nii_hdr.m

extra_nii_hdr.m 7.9 KB
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  1. %  Decode extra NIFTI header information into hdr.extra
    2. 

  2. %
    3. 

  3. %  Usage: hdr = extra_nii_hdr(hdr)
    4. 

  4. %
    5. 

  5. %  hdr can be obtained from load_nii_hdr
    6. 

  6. %
    7. 

  7. %  NIFTI data format can be found on: http://nifti.nimh.nih.gov
    8. 

  8. %
    9. 

  9. %  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
    10. 

  10. %
    11. 

  11. function hdr = extra_nii_hdr(hdr)
    12. 

  12. 

  13.    switch hdr.dime.datatype
    14. 

  14.    case 1
    15. 

  15.       extra.NIFTI_DATATYPES = 'DT_BINARY';
    16. 

  16.    case 2
    17. 

  17.       extra.NIFTI_DATATYPES = 'DT_UINT8';
    18. 

  18.    case 4
    19. 

  19.       extra.NIFTI_DATATYPES = 'DT_INT16';
    20. 

  20.    case 8
    21. 

  21.       extra.NIFTI_DATATYPES = 'DT_INT32';
    22. 

  22.    case 16
    23. 

  23.       extra.NIFTI_DATATYPES = 'DT_FLOAT32';
    24. 

  24.    case 32
    25. 

  25.       extra.NIFTI_DATATYPES = 'DT_COMPLEX64';
    26. 

  26.    case 64
    27. 

  27.       extra.NIFTI_DATATYPES = 'DT_FLOAT64';
    28. 

  28.    case 128
    29. 

  29.       extra.NIFTI_DATATYPES = 'DT_RGB24';
    30. 

  30.    case 256
    31. 

  31.       extra.NIFTI_DATATYPES = 'DT_INT8';
    32. 

  32.    case 512
    33. 

  33.       extra.NIFTI_DATATYPES = 'DT_UINT16';
    34. 

  34.    case 768
    35. 

  35.       extra.NIFTI_DATATYPES = 'DT_UINT32';
    36. 

  36.    case 1024
    37. 

  37.       extra.NIFTI_DATATYPES = 'DT_INT64';
    38. 

  38.    case 1280
    39. 

  39.       extra.NIFTI_DATATYPES = 'DT_UINT64';
    40. 

  40.    case 1536
    41. 

  41.       extra.NIFTI_DATATYPES = 'DT_FLOAT128';
    42. 

  42.    case 1792
    43. 

  43.       extra.NIFTI_DATATYPES = 'DT_COMPLEX128';
    44. 

  44.    case 2048
    45. 

  45.       extra.NIFTI_DATATYPES = 'DT_COMPLEX256';
    46. 

  46.    otherwise
    47. 

  47.       extra.NIFTI_DATATYPES = 'DT_UNKNOWN';
    48. 

  48.    end
    49. 

  49. 

  50.    switch hdr.dime.intent_code
    51. 

  51.    case 2
    52. 

  52.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CORREL';
    53. 

  53.    case 3
    54. 

  54.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TTEST';
    55. 

  55.    case 4
    56. 

  56.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_FTEST';
    57. 

  57.    case 5
    58. 

  58.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_ZSCORE';
    59. 

  59.    case 6
    60. 

  60.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHISQ';
    61. 

  61.    case 7
    62. 

  62.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_BETA';
    63. 

  63.    case 8
    64. 

  64.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_BINOM';
    65. 

  65.    case 9
    66. 

  66.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_GAMMA';
    67. 

  67.    case 10
    68. 

  68.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_POISSON';
    69. 

  69.    case 11
    70. 

  70.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NORMAL';
    71. 

  71.    case 12
    72. 

  72.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_FTEST_NONC';
    73. 

  73.    case 13
    74. 

  74.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHISQ_NONC';
    75. 

  75.    case 14
    76. 

  76.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOGISTIC';
    77. 

  77.    case 15
    78. 

  78.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LAPLACE';
    79. 

  79.    case 16
    80. 

  80.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_UNIFORM';
    81. 

  81.    case 17
    82. 

  82.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TTEST_NONC';
    83. 

  83.    case 18
    84. 

  84.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_WEIBULL';
    85. 

  85.    case 19
    86. 

  86.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHI';
    87. 

  87.    case 20
    88. 

  88.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_INVGAUSS';
    89. 

  89.    case 21
    90. 

  90.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_EXTVAL';
    91. 

  91.    case 22
    92. 

  92.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_PVAL';
    93. 

  93.    case 23
    94. 

  94.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOGPVAL';
    95. 

  95.    case 24
    96. 

  96.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOG10PVAL';
    97. 

  97.    case 1001
    98. 

  98.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_ESTIMATE';
    99. 

  99.    case 1002
    100. 

  100.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LABEL';
    101. 

  101.    case 1003
    102. 

  102.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NEURONAME';
    103. 

  103.    case 1004
    104. 

  104.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_GENMATRIX';
    105. 

  105.    case 1005
    106. 

  106.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_SYMMATRIX';
    107. 

  107.    case 1006
    108. 

  108.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_DISPVECT';
    109. 

  109.    case 1007
    110. 

  110.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_VECTOR';
    111. 

  111.    case 1008
    112. 

  112.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_POINTSET';
    113. 

  113.    case 1009
    114. 

  114.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TRIANGLE';
    115. 

  115.    case 1010
    116. 

  116.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_QUATERNION';
    117. 

  117.    case 1011
    118. 

  118.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_DIMLESS';
    119. 

  119.    otherwise
    120. 

  120.       extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NONE';
    121. 

  121.    end
    122. 

  122. 

  123.    extra.NIFTI_INTENT_NAMES = hdr.hist.intent_name;
    124. 

  124. 

  125.    if hdr.hist.sform_code > 0
    126. 

  126.       switch hdr.hist.sform_code
    127. 

  127.       case 1
    128. 

  128.          extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_SCANNER_ANAT';
    129. 

  129.       case 2
    130. 

  130.          extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_ALIGNED_ANAT';
    131. 

  131.       case 3
    132. 

  132.          extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_TALAIRACH';
    133. 

  133.       case 4
    134. 

  134.          extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_MNI_152';
    135. 

  135.       otherwise
    136. 

  136.          extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
    137. 

  137.       end
    138. 

  138. 

  139.       extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
    140. 

  140.    elseif hdr.hist.qform_code > 0
    141. 

  141.       extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
    142. 

  142. 

  143.       switch hdr.hist.qform_code
    144. 

  144.       case 1
    145. 

  145.          extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_SCANNER_ANAT';
    146. 

  146.       case 2
    147. 

  147.          extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_ALIGNED_ANAT';
    148. 

  148.       case 3
    149. 

  149.          extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_TALAIRACH';
    150. 

  150.       case 4
    151. 

  151.          extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_MNI_152';
    152. 

  152.       otherwise
    153. 

  153.          extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
    154. 

  154.       end
    155. 

  155.    else
    156. 

  156.       extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
    157. 

  157.       extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
    158. 

  158.    end
    159. 

  159. 

  160.    switch bitand(hdr.dime.xyzt_units, 7)	% mask with 0x07
    161. 

  161.    case 1
    162. 

  162.       extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_METER';
    163. 

  163.    case 2
    164. 

  164.       extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_MM';	% millimeter
    165. 

  165.    case 3
    166. 

  166.       extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_MICRO';
    167. 

  167.    otherwise
    168. 

  168.       extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_UNKNOWN';
    169. 

  169.    end
    170. 

  170. 

  171.    switch bitand(hdr.dime.xyzt_units, 56)	% mask with 0x38
    172. 

  172.    case 8
    173. 

  173.       extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_SEC';
    174. 

  174.    case 16
    175. 

  175.       extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_MSEC';
    176. 

  176.    case 24
    177. 

  177.       extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_USEC';	% microsecond
    178. 

  178.    otherwise
    179. 

  179.       extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_UNKNOWN';
    180. 

  180.    end
    181. 

  181. 

  182.    switch hdr.dime.xyzt_units
    183. 

  183.    case 32
    184. 

  184.       extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_HZ';
    185. 

  185.    case 40
    186. 

  186.       extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_PPM';	% part per million
    187. 

  187.    case 48
    188. 

  188.       extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_RADS';	% radians per second
    189. 

  189.    otherwise
    190. 

  190.       extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_UNKNOWN';
    191. 

  191.    end
    192. 

  192. 

  193.    %  MRI-specific spatial and temporal information
    194. 

  194.    %
    195. 

  195.    dim_info = hdr.hk.dim_info;
    196. 

  196.    extra.NIFTI_FREQ_DIM = bitand(dim_info, 3);
    197. 

  197.    extra.NIFTI_PHASE_DIM = bitand(bitshift(dim_info, -2), 3);
    198. 

  198.    extra.NIFTI_SLICE_DIM = bitand(bitshift(dim_info, -4), 3);
    199. 

  199. 

  200.    %  Check slice code
    201. 

  201.    %
    202. 

  202.    switch hdr.dime.slice_code
    203. 

  203.    case 1
    204. 

  204.       extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_SEQ_INC';	% sequential increasing
    205. 

  205.    case 2
    206. 

  206.       extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_SEQ_DEC';	% sequential decreasing
    207. 

  207.    case 3
    208. 

  208.       extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_INC';	% alternating increasing
    209. 

  209.    case 4
    210. 

  210.       extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_DEC';	% alternating decreasing
    211. 

  211.    case 5
    212. 

  212.       extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_INC2';	% ALT_INC # 2
    213. 

  213.    case 6
    214. 

  214.       extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_DEC2';	% ALT_DEC # 2
    215. 

  215.    otherwise
    216. 

  216.       extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_UNKNOWN';
    217. 

  217.    end
    218. 

  218. 

  219.    %  Check NIFTI version
    220. 

  220.    %
    221. 

  221.    if     ~isempty(hdr.hist.magic) & strcmp(hdr.hist.magic(1),'n') & ...
    222. 

  222. 	( strcmp(hdr.hist.magic(2),'i') | strcmp(hdr.hist.magic(2),'+') ) & ...
    223. 

  223. 	  str2num(hdr.hist.magic(3)) >= 1 & str2num(hdr.hist.magic(3)) <= 9
    224. 

  224. 

  225.       extra.NIFTI_VERSION = str2num(hdr.hist.magic(3));
    226. 

  226.    else
    227. 

  227.       extra.NIFTI_VERSION = 0;
    228. 

  228.    end
    229. 

  229. 

  230.    %  Check if data stored in the same file (*.nii) or separate
    231. 

  231.    %  files (*.hdr/*.img)
    232. 

  232.    %
    233. 

  233.    if isempty(hdr.hist.magic)
    234. 

  234.       extra.NIFTI_ONEFILE = 0;
    235. 

  235.    else
    236. 

  236.       extra.NIFTI_ONEFILE = strcmp(hdr.hist.magic(2), '+');
    237. 

  237.    end
    238. 

  238. 

  239.    %  Swap has been taken care of by checking whether sizeof_hdr is
    240. 

  240.    %  348 (machine is 'ieee-le' or 'ieee-be' etc)
    241. 

  241.    %
    242. 

  242.    % extra.NIFTI_NEEDS_SWAP = (hdr.dime.dim(1) < 0 | hdr.dime.dim(1) > 7);
    243. 

  243. 

  244.    %  Check NIFTI header struct contains a 5th (vector) dimension
    245. 

  245.    %
    246. 

  246.    if hdr.dime.dim(1) > 4 & hdr.dime.dim(6) > 1
    247. 

  247.       extra.NIFTI_5TH_DIM = hdr.dime.dim(6);
    248. 

  248.    else
    249. 

  249.       extra.NIFTI_5TH_DIM = 0;
    250. 

  250.    end
    251. 

  251. 

  252.    hdr.extra = extra;
    253. 

  253. 

  254.    return;					% extra_nii_hdr
    255. 

  255.