Hi Doug,

Thanks for your help. I got the attached output for the MD calculation - do you know if these are reasonable results ? how come the values of the corpus-callosum so different ?

CC results -

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 35 251 449 449.0 CC_Posterior 5.9866 7.7511 0.0000 16.0000 16.0000 36 252 237 237.0 CC_Mid_Posterior 183.9494 785.5627 0.0000 5001.0000 5001.0000 37 253 174 174.0 CC_Central 1587.2874 2217.3154 0.0000 5002.0000 5002.0000 38 254 210 210.0 CC_Mid_Anterior 1338.9333 1656.6611 0.0000 5002.0000 5002.0000 39 255 401 401.0 CC_Anterior 1340.8704 920.4716 0.0000 3028.0000 3028.0000

All results-

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 0 16263767 16263767.0 Unknown 105.0203 555.8546 0.0000 5002.0000 5002.0000 2 4 1429 1429.0 Left-Lateral-Ventricle 1205.2814 1696.0261 0.0000 5001.0000 5001.0000 3 5 61 61.0 Left-Inf-Lat-Vent 1651.1803 1050.3809 0.0000 5001.0000 5001.0000 4 7 8733 8733.0 Left-Cerebellum-White-Matter 303.9889 692.3320 0.0000 3013.0000 3013.0000 5 8 35697 35697.0 Left-Cerebellum-Cortex 328.1487 800.4635 0.0000 3016.0000 3016.0000 6 10 5586 5586.0 Left-Thalamus-Proper 776.9293 1738.6683 0.0000 5001.0000 5001.0000 7 11 2003 2003.0 Left-Caudate 3098.6599 2212.4736 0.0000 5001.0000 5001.0000 8 12 4464 4464.0 Left-Putamen 3184.5918 1929.2238 0.0000 5001.0000 5001.0000 9 13 726 726.0 Left-Pallidum 3507.9766 2168.7949 4.0000 5001.0000 4997.0000 10 14 57 57.0 3rd-Ventricle 1272.3158 2118.5652 0.0000 5001.0000 5001.0000 11 15 747 747.0 4th-Ventricle 39.2918 136.0397 0.0000 1013.0000 1013.0000 12 16 15338 15338.0 Brain-Stem 887.5380 1201.0325 0.0000 5002.0000 5002.0000 13 17 2316 2316.0 Left-Hippocampus 2519.1814 2068.5225 0.0000 5001.0000 5001.0000 14 18 937 937.0 Left-Amygdala 3112.2273 1532.0126 0.0000 5001.0000 5001.0000 15 24 243 243.0 CSF 139.6379 706.3411 0.0000 5002.0000 5002.0000 16 26 431 431.0 Left-Accumbens-area 2903.3179 548.7380 1023.0000 5001.0000 3978.0000 17 28 1892 1892.0 Left-VentralDC 1104.6935 1975.9153 0.0000 5001.0000 5001.0000 18 30 18 18.0 Left-vessel 2812.7778 646.7617 1035.0000 3035.0000 2000.0000 19 31 264 264.0 Left-choroid-plexus 740.3864 1035.1217 0.0000 5001.0000 5001.0000 20 43 1486 1486.0 Right-Lateral-Ventricle 1163.9320 1678.3546 0.0000 5002.0000 5002.0000 21 44 66 66.0 Right-Inf-Lat-Vent 4869.5908 335.7767 4031.0000 5002.0000 971.0000 22 46 9063 9063.0 Right-Cerebellum-White-Matter 528.6555 1037.6643 0.0000 4013.0000 4013.0000 23 47 32805 32805.0 Right-Cerebellum-Cortex 348.7231 902.4393 0.0000 4013.0000 4013.0000 24 49 5262 5262.0 Right-Thalamus-Proper 625.0261 1578.8838 0.0000 5002.0000 5002.0000 25 50 2143 2143.0 Right-Caudate 2655.9062 1884.6532 0.0000 5002.0000 5002.0000 26 51 4344 4344.0 Right-Putamen 4297.2183 1264.8182 43.0000 5002.0000 4959.0000 27 52 921 921.0 Right-Pallidum 2260.4006 2455.9590 43.0000 5002.0000 4959.0000 28 53 2515 2515.0 Right-Hippocampus 2451.9885 2322.6428 0.0000 5002.0000 5002.0000 29 54 1121 1121.0 Right-Amygdala 3649.0322 2089.6423 43.0000 5002.0000 4959.0000 30 58 341 341.0 Right-Accumbens-area 2160.9326 1494.9885 0.0000 4023.0000 4023.0000 31 60 2309 2309.0 Right-VentralDC 856.0403 1765.5569 0.0000 5002.0000 5002.0000 32 62 17 17.0 Right-vessel 4945.1177 234.5327 4035.0000 5002.0000 967.0000 33 63 195 195.0 Right-choroid-plexus 1060.4257 1698.5687 0.0000 5002.0000 5002.0000 34 85 17 17.0 Optic-Chiasm 374.4706 610.2134 0.0000 2023.0000 2023.0000 35 251 449 449.0 CC_Posterior 5.9866 7.7511 0.0000 16.0000 16.0000 36 252 237 237.0 CC_Mid_Posterior 183.9494 785.5627 0.0000 5001.0000 5001.0000 37 253 174 174.0 CC_Central 1587.2874 2217.3154 0.0000 5002.0000 5002.0000 38 254 210 210.0 CC_Mid_Anterior 1338.9333 1656.6611 0.0000 5002.0000 5002.0000 39 255 401 401.0 CC_Anterior 1340.8704 920.4716 0.0000 3028.0000 3028.0000 40 1000 24 24.0 ctx-lh-unknown 5001.0000 -nan 5001.0000 5001.0000 0.0000 41 1001 854 854.0 ctx-lh-bankssts 218.2401 534.4711 0.0000 3009.0000 3009.0000 42 1002 421 421.0 ctx-lh-caudalanteriorcingulate 2067.9407 1589.9967 0.0000 5001.0000 5001.0000 43 1003 3160 3160.0 ctx-lh-caudalmiddlefrontal 1924.0532 1171.6512 0.0000 5001.0000 5001.0000 44 1005 497 497.0 ctx-lh-cuneus 0.0000 0.0000 0.0000 0.0000 0.0000 45 1006 618 618.0 ctx-lh-entorhinal 3607.0874 1856.6394 0.0000 5001.0000 5001.0000 46 1007 3182 3182.0 ctx-lh-fusiform 1484.3463 1486.4078 0.0000 5001.0000 5001.0000 47 1008 4949 4949.0 ctx-lh-inferiorparietal 6.5112 80.7200 0.0000 1007.0000 1007.0000 48 1009 3357 3357.0 ctx-lh-inferiortemporal 823.0471 1069.3124 0.0000 3031.0000 3031.0000 49 1010 876 876.0 ctx-lh-isthmuscingulate 7.8413 7.7702 0.0000 16.0000 16.0000 50 1011 2523 2523.0 ctx-lh-lateraloccipital 0.2029 1.2581 0.0000 8.0000 8.0000 51 1012 2879 2879.0 ctx-lh-lateralorbitofrontal 1774.3990 1452.4291 0.0000 5001.0000 5001.0000 52 1013 1962 1962.0 ctx-lh-lingual 6.9760 5.2759 0.0000 47.0000 47.0000 53 1014 1714 1714.0 ctx-lh-medialorbitofrontal 1330.5485 1269.4579 0.0000 5001.0000 5001.0000 54 1015 4145 4145.0 ctx-lh-middletemporal 851.2019 1035.8433 0.0000 3031.0000 3031.0000 55 1016 811 811.0 ctx-lh-parahippocampal 1237.8545 1632.6826 0.0000 5001.0000 5001.0000 56 1017 1031 1031.0 ctx-lh-paracentral 163.8759 464.2348 0.0000 3014.0000 3014.0000 57 1018 1511 1511.0 ctx-lh-parsopercularis 1511.6346 1118.9261 0.0000 3027.0000 3027.0000 58 1019 793 793.0 ctx-lh-parsorbitalis 308.1538 665.0723 0.0000 3024.0000 3024.0000 59 1020 1487 1487.0 ctx-lh-parstriangularis 1024.8049 1068.4369 0.0000 5001.0000 5001.0000 60 1021 362 362.0 ctx-lh-pericalcarine 0.1768 1.6749 0.0000 16.0000 16.0000 61 1022 2404 2404.0 ctx-lh-postcentral 230.2013 565.3003 0.0000 3030.0000 3030.0000 62 1023 837 837.0 ctx-lh-posteriorcingulate 365.9355 763.2245 0.0000 3026.0000 3026.0000 63 1024 5058 5058.0 ctx-lh-precentral 697.4423 964.1465 0.0000 3030.0000 3030.0000 64 1025 2900 2900.0 ctx-lh-precuneus 0.3721 2.4073 0.0000 16.0000 16.0000 65 1026 968 968.0 ctx-lh-rostralanteriorcingulate 1851.4866 1085.8788 0.0000 3028.0000 3028.0000 66 1027 5944 5944.0 ctx-lh-rostralmiddlefrontal 637.7747 985.5963 0.0000 3028.0000 3028.0000 67 1028 9845 9845.0 ctx-lh-superiorfrontal 1617.2528 1355.0308 0.0000 5001.0000 5001.0000 68 1029 3901 3901.0 ctx-lh-superiorparietal 45.0510 249.0687 0.0000 3007.0000 3007.0000 69 1030 5179 5179.0 ctx-lh-superiortemporal 1407.5188 1191.6757 0.0000 5001.0000 5001.0000 70 1031 4343 4343.0 ctx-lh-supramarginal 492.8904 936.2776 0.0000 3033.0000 3033.0000 71 1032 202 202.0 ctx-lh-frontalpole 0.0000 0.0000 0.0000 0.0000 0.0000 72 1033 1041 1041.0 ctx-lh-temporalpole 2141.6599 1133.5350 0.0000 5001.0000 5001.0000 73 1034 372 372.0 ctx-lh-transversetemporal 1850.0807 1024.5981 0.0000 5001.0000 5001.0000 74 1035 2899 2899.0 ctx-lh-insula 2277.8611 1366.0648 0.0000 5001.0000 5001.0000 75 2000 138 138.0 ctx-rh-unknown 4081.4709 1066.3595 43.0000 5002.0000 4959.0000 76 2001 751 751.0 ctx-rh-bankssts 2120.9041 1563.7277 0.0000 4015.0000 4015.0000 77 2002 856 856.0 ctx-rh-caudalanteriorcingulate 1341.9065 1345.1031 0.0000 5002.0000 5002.0000 78 2003 2573 2573.0 ctx-rh-caudalmiddlefrontal 3033.8103 1231.6836 0.0000 5002.0000 5002.0000 79 2005 524 524.0 ctx-rh-cuneus 0.0000 0.0000 0.0000 0.0000 0.0000 80 2006 410 410.0 ctx-rh-entorhinal 4432.1440 723.8027 43.0000 5002.0000 4959.0000 81 2007 3196 3196.0 ctx-rh-fusiform 2248.0046 1983.5382 0.0000 5002.0000 5002.0000 82 2008 5482 5482.0 ctx-rh-inferiorparietal 47.2470 342.8887 0.0000 4009.0000 4009.0000 83 2009 3422 3422.0 ctx-rh-inferiortemporal 2445.4734 1710.7948 0.0000 5002.0000 5002.0000 84 2010 799 799.0 ctx-rh-isthmuscingulate 11.3517 13.3818 0.0000 46.0000 46.0000 85 2011 2898 2898.0 ctx-rh-lateraloccipital 1.3623 7.8864 0.0000 47.0000 47.0000 86 2012 2711 2711.0 ctx-rh-lateralorbitofrontal 2557.2144 1550.0718 0.0000 5002.0000 5002.0000 87 2013 2155 2155.0 ctx-rh-lingual 36.0097 129.2816 0.0000 2007.0000 2007.0000 88 2014 2138 2138.0 ctx-rh-medialorbitofrontal 657.1188 977.1573 0.0000 4028.0000 4028.0000 89 2015 4142 4142.0 ctx-rh-middletemporal 1941.5190 1535.4354 0.0000 4031.0000 4031.0000 90 2016 700 700.0 ctx-rh-parahippocampal 2320.7200 1722.3994 0.0000 5002.0000 5002.0000 91 2017 1416 1416.0 ctx-rh-paracentral 1129.2288 1324.3389 0.0000 4014.0000 4014.0000 92 2018 1076 1076.0 ctx-rh-parsopercularis 2799.9099 1442.7355 0.0000 5002.0000 5002.0000 93 2019 795 795.0 ctx-rh-parsorbitalis 938.1031 1388.8167 0.0000 4024.0000 4024.0000 94 2020 1307 1307.0 ctx-rh-parstriangularis 1947.5524 1547.6558 0.0000 4028.0000 4028.0000 95 2021 414 414.0 ctx-rh-pericalcarine 0.0000 0.0000 0.0000 0.0000 0.0000 96 2022 2549 2549.0 ctx-rh-postcentral 1229.1384 1388.3079 0.0000 4034.0000 4034.0000 97 2023 901 901.0 ctx-rh-posteriorcingulate 522.5083 1161.7966 0.0000 5002.0000 5002.0000 98 2024 4605 4605.0 ctx-rh-precentral 1467.4482 1491.9133 0.0000 4035.0000 4035.0000 99 2025 3024 3024.0 ctx-rh-precuneus 1.0999 4.9147 0.0000 46.0000 46.0000 100 2026 924 924.0 ctx-rh-rostralanteriorcingulate 651.9740 888.0228 0.0000 4028.0000 4028.0000 101 2027 6470 6470.0 ctx-rh-rostralmiddlefrontal 1012.6683 1376.5038 0.0000 4028.0000 4028.0000 102 2028 9798 9798.0 ctx-rh-superiorfrontal 2197.2322 1592.8611 0.0000 5002.0000 5002.0000 103 2029 3746 3746.0 ctx-rh-superiorparietal 175.9952 667.3113 0.0000 4033.0000 4033.0000 104 2030 5304 5304.0 ctx-rh-superiortemporal 2633.3694 1327.8750 0.0000 5002.0000 5002.0000 105 2031 3576 3576.0 ctx-rh-supramarginal 1440.6700 1530.0399 0.0000 5002.0000 5002.0000 106 2032 325 325.0 ctx-rh-frontalpole 0.0000 0.0000 0.0000 0.0000 0.0000 107 2033 603 603.0 ctx-rh-temporalpole 3632.8491 978.0482 0.0000 5002.0000 5002.0000 108 2034 163 163.0 ctx-rh-transversetemporal 2137.0061 1348.5909 0.0000 4035.0000 4035.0000 109 2035 2857 2857.0 ctx-rh-insula 3450.0242 1476.4425 0.0000 5002.0000 5002.0000 110 3001 885 885.0 wm-lh-bankssts 221.4158 647.5278 0.0000 3009.0000 3009.0000 111 3002 1179 1179.0 wm-lh-caudalanteriorcingulate 1693.7269 1835.8118 0.0000 5001.0000 5001.0000 112 3003 4161 4161.0 wm-lh-caudalmiddlefrontal 1699.8068 1099.4926 0.0000 5001.0000 5001.0000 113 3005 480 480.0 wm-lh-cuneus 0.0000 0.0000 0.0000 0.0000 0.0000 114 3006 82 82.0 wm-lh-entorhinal 3762.0854 1140.0966 4.0000 5001.0000 4997.0000 115 3007 2578 2578.0 wm-lh-fusiform 1215.8875 1372.1278 0.0000 5001.0000 5001.0000 116 3008 4617 4617.0 wm-lh-inferiorparietal 22.2378 160.6620 0.0000 3007.0000 3007.0000 117 3009 1812 1812.0 wm-lh-inferiortemporal 1031.3306 1193.7415 0.0000 3031.0000 3031.0000 118 3010 2032 2032.0 wm-lh-isthmuscingulate 16.1855 97.1478 0.0000 1016.0000 1016.0000 119 3011 2997 2997.0 wm-lh-lateraloccipital 0.3363 1.6057 0.0000 8.0000 8.0000 120 3012 3063 3063.0 wm-lh-lateralorbitofrontal 2151.0332 1257.6028 0.0000 5001.0000 5001.0000 121 3013 2399 2399.0 wm-lh-lingual 9.0196 57.9046 0.0000 1007.0000 1007.0000 122 3014 1000 1000.0 wm-lh-medialorbitofrontal 1279.4041 1197.7087 0.0000 5001.0000 5001.0000 123 3015 1061 1061.0 wm-lh-middletemporal 1541.8662 1267.1495 0.0000 3031.0000 3031.0000 124 3016 485 485.0 wm-lh-parahippocampal 1200.3381 1504.2911 0.0000 5001.0000 5001.0000 125 3017 1419 1419.0 wm-lh-paracentral 153.4567 402.2811 0.0000 3012.0000 3012.0000 126 3018 1642 1642.0 wm-lh-parsopercularis 1965.9324 1107.3256 0.0000 3035.0000 3035.0000 127 3019 223 223.0 wm-lh-parsorbitalis 612.5202 779.3184 0.0000 3024.0000 3024.0000 128 3020 1630 1630.0 wm-lh-parstriangularis 2005.0251 1242.6742 0.0000 5001.0000 5001.0000 129 3021 1200 1200.0 wm-lh-pericalcarine 0.2133 1.7157 0.0000 16.0000 16.0000 130 3022 3343 3343.0 wm-lh-postcentral 884.3278 996.7158 0.0000 3033.0000 3033.0000 131 3023 2369 2369.0 wm-lh-posteriorcingulate 586.1232 1373.9506 0.0000 5001.0000 5001.0000 132 3024 6878 6878.0 wm-lh-precentral 795.6331 948.9272 0.0000 3035.0000 3035.0000 133 3025 3369 3369.0 wm-lh-precuneus 0.0427 0.8260 0.0000 16.0000 16.0000 134 3026 1423 1423.0 wm-lh-rostralanteriorcingulate 2465.6416 931.6223 0.0000 3028.0000 3028.0000 135 3027 5509 5509.0 wm-lh-rostralmiddlefrontal 1474.4030 1228.9650 0.0000 5001.0000 5001.0000 136 3028 10076 10076.0 wm-lh-superiorfrontal 2539.9971 1525.0880 0.0000 5001.0000 5001.0000 137 3029 5391 5391.0 wm-lh-superiorparietal 149.2150 477.9887 0.0000 3033.0000 3033.0000 138 3030 3330 3330.0 wm-lh-superiortemporal 1719.6111 1152.3683 0.0000 5001.0000 5001.0000 139 3031 4393 4393.0 wm-lh-supramarginal 1512.4888 1253.5046 0.0000 3033.0000 3033.0000 140 3032 9 9.0 wm-lh-frontalpole 0.0000 0.0000 0.0000 0.0000 0.0000 141 3033 136 136.0 wm-lh-temporalpole 1872.0515 1192.4773 0.0000 3031.0000 3031.0000 142 3034 327 327.0 wm-lh-transversetemporal 2253.0886 1308.4039 5.0000 5001.0000 4996.0000 143 3035 3806 3806.0 wm-lh-insula 1893.2344 1842.3096 0.0000 5001.0000 5001.0000 144 4001 1055 1055.0 wm-rh-bankssts 2382.6738 1306.7096 0.0000 4016.0000 4016.0000 145 4002 1626 1626.0 wm-rh-caudalanteriorcingulate 2365.9939 1754.4871 0.0000 5002.0000 5002.0000 146 4003 3274 3274.0 wm-rh-caudalmiddlefrontal 2900.4553 1251.0457 0.0000 5002.0000 5002.0000 147 4005 462 462.0 wm-rh-cuneus 0.0000 0.0000 0.0000 0.0000 0.0000 148 4006 106 106.0 wm-rh-entorhinal 3299.4058 1537.5352 43.0000 5002.0000 4959.0000 149 4007 2257 2257.0 wm-rh-fusiform 1534.2335 1856.6631 0.0000 5002.0000 5002.0000 150 4008 4279 4279.0 wm-rh-inferiorparietal 298.4765 778.5995 0.0000 4009.0000 4009.0000 151 4009 1746 1746.0 wm-rh-inferiortemporal 2093.4932 1636.5851 0.0000 5002.0000 5002.0000 152 4010 1740 1740.0 wm-rh-isthmuscingulate 38.8356 243.3854 0.0000 2016.0000 2016.0000 153 4011 2606 2606.0 wm-rh-lateraloccipital 0.3427 3.9993 0.0000 47.0000 47.0000 154 4012 2949 2949.0 wm-rh-lateralorbitofrontal 2979.5647 1360.8296 0.0000 5002.0000 5002.0000 155 4013 2344 2344.0 wm-rh-lingual 69.8114 372.1888 0.0000 4007.0000 4007.0000 156 4014 1302 1302.0 wm-rh-medialorbitofrontal 2224.4915 1450.4080 0.0000 4028.0000 4028.0000 157 4015 1691 1691.0 wm-rh-middletemporal 2155.5742 1632.5012 0.0000 5002.0000 5002.0000 158 4016 414 414.0 wm-rh-parahippocampal 2000.5846 1798.7676 0.0000 5002.0000 5002.0000 159 4017 2204 2204.0 wm-rh-paracentral 1233.0594 1383.9352 0.0000 4014.0000 4014.0000 160 4018 1397 1397.0 wm-rh-parsopercularis 3697.2634 1052.3094 0.0000 5002.0000 5002.0000 161 4019 349 349.0 wm-rh-parsorbitalis 1171.5272 1165.5026 0.0000 4003.0000 4003.0000 162 4020 1450 1450.0 wm-rh-parstriangularis 2595.8911 1333.6057 0.0000 5002.0000 5002.0000 163 4021 1072 1072.0 wm-rh-pericalcarine 0.0000 0.0000 0.0000 0.0000 0.0000 164 4022 3537 3537.0 wm-rh-postcentral 1828.3132 1400.6344 0.0000 4035.0000 4035.0000 165 4023 2235 2235.0 wm-rh-posteriorcingulate 674.7817 1563.4506 0.0000 5002.0000 5002.0000 166 4024 6263 6263.0 wm-rh-precentral 1554.2966 1416.0610 0.0000 4035.0000 4035.0000 167 4025 3400 3400.0 wm-rh-precuneus 17.1824 184.4637 0.0000 2007.0000 2007.0000 168 4026 1047 1047.0 wm-rh-rostralanteriorcingulate 1860.3477 1164.7131 0.0000 4028.0000 4028.0000 169 4027 5332 5332.0 wm-rh-rostralmiddlefrontal 2273.0229 1726.8505 0.0000 5002.0000 5002.0000 170 4028 9343 9343.0 wm-rh-superiorfrontal 3128.9961 1617.0729 0.0000 5002.0000 5002.0000 171 4029 5015 5015.0 wm-rh-superiorparietal 700.2903 1143.9926 0.0000 4033.0000 4033.0000 172 4030 2331 2331.0 wm-rh-superiortemporal 3029.0220 1305.0964 0.0000 5002.0000 5002.0000 173 4031 4879 4879.0 wm-rh-supramarginal 2473.6401 1590.3677 0.0000 5002.0000 5002.0000 174 4032 64 64.0 wm-rh-frontalpole 0.0000 0.0000 0.0000 0.0000 0.0000 175 4033 149 149.0 wm-rh-temporalpole 2900.0806 1074.6902 0.0000 4031.0000 4031.0000 176 4034 197 197.0 wm-rh-transversetemporal 2931.1321 1435.5095 0.0000 5002.0000 5002.0000 177 4035 3833 3833.0 wm-rh-insula 2861.4229 2209.4307 41.0000 5002.0000 4961.0000 178 5001 17178 17178.0 Left-UnsegmentedWhiteMatter 1464.7604 1875.4178 0.0000 5001.0000 5001.0000 179 5002 18204 18204.0 Right-UnsegmentedWhiteMatter 1945.1401 2139.9580 0.0000 5002.0000 5002.0000

Thanks Rotem

I would use step 3 for the wmparc instead of vol2vol.

you need both --seg and --seg-erode

--seg-erode 1 --seg /usr/local/freesurfer/ subjects/Anatomy0981/mri/wmparc2diff.mgz

doug

On 03/20/2014 04:43 AM, Rotem Saar wrote:

Hi Doug,

Thanks you for directing me to my mistake in step 3 (see below new cmd line in step 3). What I did is the following -

1. dt_recon --i

/usr/local/freesurfer/subjects/Anatomy0981/DTI/I160.dcm --s Anatomy0981 --o /usr/local/freesurfer/subjects/Anatomy0981/DTI --b /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec

2. mri_vol2vol --mov

/usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii --targ /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg

3. mri_label2vol --seg

/usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz --temp /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --o /usr/local/freesurfer/subjects/Anatomy0981/mri/forMD.bshort

it created many *.bshort files

My qs:

1. Should I repeat step 3 with the wmparc.mgz or is it not necessary ?
2. How do I plot all MD values like I did before for FA values ?

trying to use -

mri_segstats --seg-erode 1 /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked

always end with the same message - it wants a segmentation volume but nothing works ("unknown")... I used aseg.mgz for example and other options - nada. However, If I omit the "-erode 1" it reports the table, but for FA values. What do I need to change in step 3 and how can I fix the last step ?

Thank you for your help

Rotem

Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel