gdevenyi
commented
2 years ago Hi, the regions were not missing, the NIFTI standard and/or software could not properly handle the volume normalization in the files (we work primarily in MINC, where these things are built into the standard).
I explicitly forced the value scaling to be off in the NIFI files and they now properly list the values from NIFTI tools:
LabelGeometryMeasures 3 nifti/mni_icbm152_t1_tal_nlin_sym_09c_labels.nii.gz
Label Volume(voxels)SurfArea(mm^2) Eccentricity Elongation Orientation Centroid Axes Length Bounding Box
1 13499 5232.55 0.90825 2.38989 1.09157 [75.9708, 137.723, 81.5086] [19.8428, 38.423, 47.4223] [61, 92, 99, 157, 64, 107]
2 2051 1078.48 0.940595 2.94524 1.00472 [76.0073, 128.51, 75.6816] [9.37926, 12.9452, 27.6241] [68, 87, 114, 141, 69, 83]
3 8335 2458.39 0.867483 2.01018 1.17431 [84.5994, 113.769, 84.6174] [16.945, 21.3023, 34.0625] [73, 94, 98, 131, 73, 97]
4 72 83.88 0.59956 1.24949 1.84272 [93.75, 123.889, 63.0417] [4.33716, 4.68285, 5.41922] [92, 96, 122, 126, 61, 65]
5 865 1137.13 0.987896 6.44672 1.08014 [87.5561, 112.668, 87.7665] [10.1269, 34.0729, 65.2853] [66, 96, 90, 136, 64, 98]
6 186 299.686 0.993725 8.94032 1.52661 [67.7581, 105.296, 69.3871] [3.19563, 7.79287, 28.5699] [64, 72, 97, 114, 62, 80]
7 1060 1509.32 0.9928 8.34846 1.64501 [68.6434, 107.411, 64.0509] [6.85554, 22.5142, 57.2332] [59, 81, 91, 125, 49, 84]
8 452 730.134 0.997352 13.7512 1.69768 [72.7876, 110.378, 60.1173] [3.52149, 12.0158, 48.4246] [66, 81, 95, 125, 48, 77]
9 738 792.019 0.993379 8.70452 1.52398 [68.1965, 109.312, 63.8157] [4.92337, 13.5743, 42.8556] [62, 80, 94, 121, 54, 81]
10 227 455.957 0.99502 10.0323 1.33494 [66.0088, 110.273, 65.0308] [3.8061, 17.8601, 38.1839] [61, 81, 95, 121, 57, 80]
11 724 1335.17 0.991486 7.67976 1.46439 [69.3577, 110.656, 62.0304] [6.48933, 21.4946, 49.8365] [60, 82, 92, 124, 50, 82]
12 595 1097.86 0.992255 8.05021 1.20204 [68.6218, 114.753, 62.0202] [6.24379, 19.8271, 50.2638] [60, 82, 90, 127, 49, 80]
13 1668 810.333 0.909178 2.40149 2.83092 [72.7002, 127.579, 57.8555] [8.58523, 14.2676, 20.6174] [63, 82, 121, 132, 48, 67]
85 13454 5219.67 0.908566 2.39383 2.05142 [116.035, 137.691, 81.4945] [19.8263, 38.4273, 47.4608] [100, 131, 99, 157, 64, 107]
86 2062 1079.07 0.94071 2.94802 2.14165 [116.017, 128.511, 75.6688] [9.39676, 12.9515, 27.7018] [105, 124, 114, 141, 69, 83]
87 8341 2464.73 0.866607 2.00404 1.97093 [107.424, 113.753, 84.6241] [16.9762, 21.3038, 34.0211] [98, 120, 98, 131, 73, 97]
88 1057 1499.28 0.992531 8.19723 1.50019 [123.448, 107.413, 64.1126] [6.97204, 22.6538, 57.1515] [111, 133, 91, 125, 49, 84]
89 457 736.206 0.997315 13.6549 1.44899 [119.263, 110.324, 60.1379] [3.55909, 12.103, 48.5992] [111, 127, 95, 125, 48, 77]
90 728 786.275 0.993353 8.68724 1.62646 [123.812, 109.321, 63.783] [4.92086, 13.6204, 42.7487] [112, 130, 94, 121, 54, 81]
91 218 437.497 0.995126 10.1404 1.83051 [125.899, 110.312, 65.0229] [3.70082, 18.36, 37.5277] [111, 132, 95, 121, 58, 80]
92 730 1344.01 0.991245 7.57366 1.67884 [122.593, 110.723, 62] [6.52854, 21.5264, 49.445] [110, 132, 92, 124, 50, 82]
93 191 305.966 0.993553 8.82104 1.60864 [124.351, 105.225, 69.4398] [3.22928, 7.91937, 28.4856] [120, 128, 97, 114, 62, 80]
94 71 82.363 0.656226 1.32527 1.25897 [98.3239, 123.915, 63.0704] [4.10993, 4.81396, 5.44676] [97, 100, 122, 126, 61, 65]
95 851 1120.15 0.987664 6.38623 2.05378 [104.358, 112.723, 87.7626] [10.1538, 34.2753, 64.8445] [96, 126, 90, 136, 64, 98]
96 603 1107.05 0.991603 7.73257 1.94341 [123.277, 115.078, 61.7927] [6.4543, 20.079, 49.9083] [110, 133, 90, 127, 49, 80]
97 1683 810.985 0.906359 2.36681 0.307403 [119.283, 127.608, 57.877] [8.66967, 14.2794, 20.5195] [110, 129, 121, 133, 48, 67]
Hello! based on the label lookup table here I was wondering why some of the regions are not present in the file here.
The only regions I see in the nifti file are [0, 1, 3, 4, 6, 7, 9, 11, 12, 84, 85, 87, 89, 90, 92, 93, 95, 97]