Hi Ani
using sphere is as close as we come to equal area. The difference in Gaussian curvature between the sphere and the cortex make this a non-trivial problem.
cheers Bruce
On Fri, 25 Aug 2017, Aniqa Dalowr wrote:
Also I tried using both lh.sphere and lh.sphere.reg and in both cases, the patches arent equal in surface area. There is a lot of variablility in surface area and the number of vertices. Please see below. Is there a way to generate roughly equal size patches ? Thank you,
Ani
USING lh.sphere in the mris_make_face_parcellation step
mris_anatomical_stats -a lh.ic1.annot -b bert lh
computing statistics for each annotation in lh.ic1.annot.
reading volume /Applications/freesurfer5.3/subjects//bert/mri/wm.mgz...
reading input surface /Applications/freesurfer5.3/subjects//bert/surf/lh.white...
reading input pial surface /Applications/freesurfer5.3/subjects//bert/surf/lh.pial...
reading input white surface /Applications/freesurfer5.3/subjects//bert/surf/lh.white...
reading colortable from annotation file...
colortable with 42 entries read (originally /Applications/freesurfer5.3/lib/bem/ic1.tri)
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
3003 1916 5416 2.489 1.079 0.119 0.043 36 5.9 ic1.tri_vertex_0
1834 1136 3495 2.706 0.877 0.125 0.098 33 9.1 ic1.tri_vertex_1
3900 2607 7660 2.589 0.719 0.138 0.047 65 7.2 ic1.tri_vertex_2
2642 1817 6685 3.022 0.701 0.138 0.051 38 5.3 ic1.tri_vertex_3
2584 1723 4305 2.325 0.647 0.128 0.041 30 4.5 ic1.tri_vertex_4
2920 1857 5725 2.444 0.597 0.140 0.055 48 5.8 ic1.tri_vertex_5
3273 2153 5148 2.275 0.701 0.133 0.042 43 5.1 ic1.tri_vertex_6
3067 2057 5496 2.511 0.899 0.121 0.034 33 4.1 ic1.tri_vertex_7
3062 2032 5701 2.577 0.760 0.122 0.036 73 4.8 ic1.tri_vertex_8
2561 1711 4119 2.324 0.843 0.122 0.036 27 3.9 ic1.tri_vertex_9
3771 2485 5211 1.996 0.686 0.150 0.053 57 8.4 ic1.tri_vertex_10
3161 2056 5323 2.256 1.418 0.115 0.063 41 10.5 ic1.tri_vertex_11
2901 1843 5209 2.442 0.744 0.116 0.048 39 6.2 ic1.tri_vertex_12
2606 1597 4923 2.738 0.690 0.122 0.059 60 8.2 ic1.tri_vertex_13
3201 2024 5676 2.518 1.156 0.120 0.046 47 6.1 ic1.tri_vertex_14
2773 1820 5356 2.494 0.709 0.138 0.048 52 5.7 ic1.tri_vertex_15
3014 2009 5838 2.448 0.607 0.137 0.042 40 4.7 ic1.tri_vertex_16
2830 1831 4750 2.330 1.164 0.121 0.048 56 4.5 ic1.tri_vertex_17
2562 1688 4790 2.399 0.625 0.137 0.041 34 4.2 ic1.tri_vertex_18
3426 2311 6400 2.410 1.448 0.136 0.148 151 12.1 ic1.tri_vertex_19
3174 2114 7074 2.738 1.159 0.133 0.069 57 6.4 ic1.tri_vertex_20
4168 2800 10961 3.074 0.904 0.146 0.150 130 9.4 ic1.tri_vertex_21
3168 2152 6826 2.749 0.684 0.124 0.036 36 4.7 ic1.tri_vertex_22
4735 3193 10350 2.681 0.653 0.152 0.057 91 11.0 ic1.tri_vertex_23
2135 1433 3968 2.511 0.727 0.126 0.044 24 3.6 ic1.tri_vertex_24
2722 1839 5346 2.594 0.871 0.121 0.034 30 3.5 ic1.tri_vertex_25
2334 1517 3672 2.380 0.830 0.129 0.043 128 3.7 ic1.tri_vertex_26
3167 2082 5127 2.295 0.600 0.136 0.046 41 6.1 ic1.tri_vertex_27
3160 2112 5358 2.452 0.916 0.125 0.040 39 5.1 ic1.tri_vertex_28
4252 2749 6928 2.203 0.636 0.143 0.051 64 9.0 ic1.tri_vertex_29
4375 2865 6826 2.199 0.646 0.132 0.042 54 7.4 ic1.tri_vertex_30
5192 3235 7301 2.004 0.656 0.161 0.080 95 19.8 ic1.tri_vertex_31
2115 1377 3391 2.411 0.762 0.126 0.048 59 4.0 ic1.tri_vertex_32
2403 1622 5521 2.877 0.790 0.131 0.045 28 4.2 ic1.tri_vertex_33
2128 1400 3425 2.400 1.097 0.119 0.036 24 3.3 ic1.tri_vertex_34
4474 2989 9551 2.636 0.632 0.153 0.087 1057 21.4 ic1.tri_vertex_35
3590 2437 6230 2.517 0.832 0.128 0.037 40 5.4 ic1.tri_vertex_36
3845 2558 6271 2.349 1.188 0.112 0.046 56 8.7 ic1.tri_vertex_37
2913 2084 6148 2.577 1.276 0.129 0.069 51 10.8 ic1.tri_vertex_38
4012 2586 6930 2.363 0.945 0.134 0.051 62 7.5 ic1.tri_vertex_39
3217 2108 4696 2.173 1.013 0.131 0.045 41 5.3 ic1.tri_vertex_40
2713 1785 4349 2.408 1.149 0.108 0.038 28 3.5 ic1.tri_vertex_41
USING sphere.reg in the mris_make_face_parcellation step
mris_anatomical_stats -a lh.ic1.annot -b bert lh
computing statistics for each annotation in lh.ic1.annot.
reading volume /Applications/freesurfer5.3/subjects//bert/mri/wm.mgz...
reading input surface /Applications/freesurfer5.3/subjects//bert/surf/lh.white...
reading input pial surface /Applications/freesurfer5.3/subjects//bert/surf/lh.pial...
reading input white surface /Applications/freesurfer5.3/subjects//bert/surf/lh.white...
reading colortable from annotation file...
colortable with 42 entries read (originally /Applications/freesurfer5.3/lib/bem/ic1.tri)
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
2584 1657 5000 2.640 1.040 0.120 0.041 30 4.4 ic1.tri_vertex_0
2173 1376 3765 2.450 1.215 0.114 0.088 43 5.0 ic1.tri_vertex_1
4114 2767 8489 2.654 0.747 0.141 0.049 68 7.9 ic1.tri_vertex_2
2252 1523 5735 3.015 0.666 0.136 0.052 32 4.1 ic1.tri_vertex_3
3489 2298 5803 2.350 0.626 0.129 0.041 39 6.1 ic1.tri_vertex_4
2291 1447 4650 2.511 0.584 0.140 0.054 38 4.3 ic1.tri_vertex_5
3069 2027 5018 2.342 0.656 0.127 0.045 36 4.4 ic1.tri_vertex_6
3280 2185 6272 2.596 0.822 0.122 0.036 36 4.6 ic1.tri_vertex_7
2793 1862 5136 2.564 0.802 0.120 0.035 70 4.2 ic1.tri_vertex_8
3018 2006 4855 2.367 0.915 0.121 0.053 48 8.4 ic1.tri_vertex_9
4496 2879 6014 1.969 0.655 0.158 0.060 72 11.7 ic1.tri_vertex_10
2780 1798 4086 2.171 1.348 0.112 0.036 30 3.9 ic1.tri_vertex_11
2449 1559 4574 2.538 0.761 0.117 0.042 31 4.6 ic1.tri_vertex_12
2663 1645 4811 2.653 0.706 0.123 0.059 61 8.3 ic1.tri_vertex_13
2646 1687 4989 2.629 1.017 0.122 0.047 38 5.3 ic1.tri_vertex_14
2772 1778 5350 2.498 0.725 0.135 0.057 53 7.5 ic1.tri_vertex_15
3321 2222 6174 2.399 0.609 0.135 0.040 43 4.9 ic1.tri_vertex_16
2587 1682 4071 2.241 1.268 0.119 0.049 33 4.7 ic1.tri_vertex_17
2490 1638 4703 2.407 0.655 0.137 0.042 56 4.1 ic1.tri_vertex_18
3013 2014 5542 2.389 1.494 0.132 0.093 123 9.0 ic1.tri_vertex_19
3558 2361 7437 2.711 1.091 0.133 0.108 78 9.1 ic1.tri_vertex_20
3877 2642 10218 3.067 0.849 0.143 0.151 119 8.1 ic1.tri_vertex_21
2764 1886 6179 2.792 0.694 0.126 0.036 32 4.4 ic1.tri_vertex_22
4841 3245 10279 2.666 0.644 0.149 0.056 89 10.9 ic1.tri_vertex_23
2447 1635 4160 2.408 0.766 0.123 0.042 27 3.8 ic1.tri_vertex_24
3231 2207 6247 2.577 0.901 0.121 0.034 35 4.1 ic1.tri_vertex_25
2712 1782 4440 2.424 0.820 0.130 0.041 133 4.3 ic1.tri_vertex_26
2493 1651 3941 2.240 0.620 0.135 0.047 32 4.6 ic1.tri_vertex_27
3221 2160 5530 2.401 0.866 0.131 0.042 44 5.5 ic1.tri_vertex_28
2861 1868 4979 2.278 0.629 0.139 0.049 42 6.1 ic1.tri_vertex_29
3848 2533 6384 2.237 0.626 0.134 0.043 50 7.0 ic1.tri_vertex_30
5010 3161 6623 1.960 0.649 0.153 0.062 81 12.7 ic1.tri_vertex_31
2121 1339 3709 2.530 0.675 0.127 0.070 27 8.2 ic1.tri_vertex_32
2595 1780 6760 3.033 0.775 0.145 0.053 38 5.6 ic1.tri_vertex_33
2171 1423 3370 2.315 0.978 0.117 0.041 57 3.9 ic1.tri_vertex_34
4394 2929 9412 2.626 0.640 0.155 0.088 1058 21.1 ic1.tri_vertex_35
3497 2360 6031 2.517 0.829 0.128 0.037 39 5.2 ic1.tri_vertex_36
5280 3516 8942 2.291 1.352 0.112 0.048 59 12.4 ic1.tri_vertex_37
2863 1992 5636 2.570 1.269 0.125 0.072 50 11.0 ic1.tri_vertex_38
4379 2793 7687 2.335 0.768 0.144 0.071 77 14.0 ic1.tri_vertex_39
3561 2357 5512 2.250 0.866 0.139 0.047 49 6.4 ic1.tri_vertex_40
3079 2042 4960 2.378 1.119 0.117 0.038 38 4.7 ic1.tri_vertex_41
On Fri, Aug 25, 2017 at 3:16 PM, Aniqa Dalowr aniqa4pm@gmail.com wrote: Thank you for your quick reply. This is dividing the cortex into 642 patches. Is there a way to divide it into say 50 patches ? Can I specify the number ? Thank you,
Ani
On Fri, Aug 25, 2017 at 2:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: mris_make_face_parcellation should be able to do this On Fri, 25 Aug 2017, Aniqa Dalowr wrote:
Hi All, I want to divide the cortex into patches that have the ~ same surface area. Is there a quick way to do that ? Please let me know, Thanks Ani
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