# How to create mesh of a medical image

**URL:** <https://community.freefem.org/t/how-to-create-mesh-of-a-medical-image/251>\
**Category:** General Discussion\
**Created:** [February 14, 2020, 7:55pm UTC](https://community.freefem.org/t/how-to-create-mesh-of-a-medical-image/251 "2020-02-14T19:55:21Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![Emma87](https://avatars.discourse-cdn.com/v4/letter/e/e47774/32.png) [@Emma87](https://community.freefem.org/u/Emma87)\
**Post date:** [February 14, 2020, 7:55pm UTC](https://community.freefem.org/t/how-to-create-mesh-of-a-medical-image/251/1 "2020-02-14T19:55:21Z")

</div>

I am trying to create a mesh of finite elements of a medical image, I pass that format to Gmsh and then read it in FreeFem++ but I have a mistake, could you help me how to create this mesh with FreeFem, please.

This is my code:  
//mesh unstructured version ACSII-2  
//Rodar no terminal:  
//gmsh -2 -format msh2 -string ‘Mesh.SaveElementTagType=2;’ mama.geo

load “gmsh”

mesh sq = gmshload(“mama.msh”);  
plot(sq, wait = true, cmm=“Exportando\_malha\_Gmsh”);

The Gmsh file:  
//  
lc1 = 5;  
Point(1) = { 177.000000 , 252.478937 ,0 , lc1 };  
Point(2) = { 177.510050 , 254.000000 ,0 , lc1 };  
Point(3) = { 178.000000 , 255.488332 ,0 , lc1 };  
Point(4) = { 178.503309 , 257.000000 ,0 , lc1 };  
Point(5) = { 179.000000 , 258.488197 ,0 , lc1 };  
Point(6) = { 179.715569 , 260.000000 ,0 , lc1 };  
Point(7) = { 180.270890 , 261.000000 ,0 , lc1 };  
Point(8) = { 180.724259 , 263.000000 ,0 , lc1 };  
Point(9) = { 181.279331 , 264.000000 ,0 , lc1 };  
Point(10) = { 182.000000 , 265.515699 ,0 , lc1 };  
Point(11) = { 182.701592 , 267.000000 ,0 , lc1 };  
Point(12) = { 183.274872 , 268.000000 ,0 , lc1 };  
Point(13) = { 184.000000 , 269.520736 ,0 , lc1 };  
Point(14) = { 184.700018 , 271.000000 ,0 , lc1 };  
Point(15) = { 185.480041 , 272.000000 ,0 , lc1 };  
Point(16) = { 186.270932 , 273.000000 ,0 , lc1 };  
Point(17) = { 187.000000 , 274.523458 ,0 , lc1 };  
Point(18) = { 187.703792 , 276.000000 ,0 , lc1 };  
Point(19) = { 188.278432 , 277.000000 ,0 , lc1 };  
Point(20) = { 189.000000 , 278.509987 ,0 , lc1 };  
Point(21) = { 189.709969 , 280.000000 ,0 , lc1 };  
Point(22) = { 190.279909 , 281.000000 ,0 , lc1 };  
Point(23) = { 191.000000 , 282.513712 ,0 , lc1 };  
Point(24) = { 191.708067 , 284.000000 ,0 , lc1 };  
Point(25) = { 192.488638 , 285.000000 ,0 , lc1 };  
Point(26) = { 193.272395 , 286.000000 ,0 , lc1 };  
Point(27) = { 194.000000 , 287.523945 ,0 , lc1 };  
Point(28) = { 194.701684 , 289.000000 ,0 , lc1 };  
Point(29) = { 195.273466 , 290.000000 ,0 , lc1 };  
Point(30) = { 196.000000 , 291.526432 ,0 , lc1 };  
Point(31) = { 196.697156 , 293.000000 ,0 , lc1 };  
Point(32) = { 197.270009 , 294.000000 ,0 , lc1 };  
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Point(40) = { 203.000000 , 304.524228 ,0 , lc1 };  
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Point(60) = { 217.000000 , 330.476173 ,0 , lc1 };  
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Point(74) = { 233.000000 , 342.494161 ,0 , lc1 };  
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Point(120) = { 325.000000 , 342.516592 ,0 , lc1 };  
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Point(313) = { 176.731271 , 237.000000 ,0 , lc1 };  
Point(314) = { 176.502773 , 239.000000 ,0 , lc1 };  
Point(315) = { 176.505852 , 241.000000 ,0 , lc1 };  
Point(316) = { 176.509135 , 243.000000 ,0 , lc1 };  
Point(317) = { 176.512523 , 245.000000 ,0 , lc1 };  
Point(318) = { 176.516003 , 247.000000 ,0 , lc1 };  
Point(319) = { 176.516016 , 249.000000 ,0 , lc1 };  
Point(320) = { 176.531069 , 251.000000 ,0 , lc1 };  
Line(1) = {1,2};  
Line(2) = {2,3};  
Line(3) = {3,4};  
Line(4) = {4,5};  
Line(5) = {5,6};  
Line(6) = {6,7};  
Line(7) = {7,8};  
Line(8) = {8,9};  
Line(9) = {9,10};  
Line(10) = {10,11};  
Line(11) = {11,12};  
Line(12) = {12,13};  
Line(13) = {13,14};  
Line(14) = {14,15};  
Line(15) = {15,16};  
Line(16) = {16,17};  
Line(17) = {17,18};  
Line(18) = {18,19};  
Line(19) = {19,20};  
Line(20) = {20,21};  
Line(21) = {21,22};  
Line(22) = {22,23};  
Line(23) = {23,24};  
Line(24) = {24,25};  
Line(25) = {25,26};  
Line(26) = {26,27};  
Line(27) = {27,28};  
Line(28) = {28,29};  
Line(29) = {29,30};  
Line(30) = {30,31};  
Line(31) = {31,32};  
Line(32) = {32,33};  
Line(33) = {33,34};  
Line(34) = {34,35};  
Line(35) = {35,36};  
Line(36) = {36,37};  
Line(37) = {37,38};  
Line(38) = {38,39};  
Line(39) = {39,40};  
Line(40) = {40,41};  
Line(41) = {41,42};  
Line(42) = {42,43};  
Line(43) = {43,44};  
Line(44) = {44,45};  
Line(45) = {45,46};  
Line(46) = {46,47};  
Line(47) = {47,48};  
Line(48) = {48,49};  
Line(49) = {49,50};  
Line(50) = {50,51};  
Line(51) = {51,52};  
Line(52) = {52,53};  
Line(53) = {53,54};  
Line(54) = {54,55};  
Line(55) = {55,56};  
Line(56) = {56,57};  
Line(57) = {57,58};  
Line(58) = {58,59};  
Line(59) = {59,60};  
Line(60) = {60,61};  
Line(61) = {61,62};  
Line(62) = {62,63};  
Line(63) = {63,64};  
Line(64) = {64,65};  
Line(65) = {65,66};  
Line(66) = {66,67};  
Line(67) = {67,68};  
Line(68) = {68,69};  
Line(69) = {69,70};  
Line(70) = {70,71};  
Line(71) = {71,72};  
Line(72) = {72,73};  
Line(73) = {73,74};  
Line(74) = {74,75};  
Line(75) = {75,76};  
Line(76) = {76,77};  
Line(77) = {77,78};  
Line(78) = {78,79};  
Line(79) = {79,80};  
Line(80) = {80,81};  
Line(81) = {81,82};  
Line(82) = {82,83};  
Line(83) = {83,84};  
Line(84) = {84,85};  
Line(85) = {85,86};  
Line(86) = {86,87};  
Line(87) = {87,88};  
Line(88) = {88,89};  
Line(89) = {89,90};  
Line(90) = {90,91};  
Line(91) = {91,92};  
Line(92) = {92,93};  
Line(93) = {93,94};  
Line(94) = {94,95};  
Line(95) = {95,96};  
Line(96) = {96,97};  
Line(97) = {97,98};  
Line(98) = {98,99};  
Line(99) = {99,100};  
Line(100) = {100,101};  
Line(101) = {101,102};  
Line(102) = {102,103};  
Line(103) = {103,104};  
Line(104) = {104,105};  
Line(105) = {105,106};  
Line(106) = {106,107};  
Line(107) = {107,108};  
Line(108) = {108,109};  
Line(109) = {109,110};  
Line(110) = {110,111};  
Line(111) = {111,112};  
Line(112) = {112,113};  
Line(113) = {113,114};  
Line(114) = {114,115};  
Line(115) = {115,116};  
Line(116) = {116,117};  
Line(117) = {117,118};  
Line(118) = {118,119};  
Line(119) = {119,120};  
Line(120) = {120,121};  
Line(121) = {121,122};  
Line(122) = {122,123};  
Line(123) = {123,124};  
Line(124) = {124,125};  
Line(125) = {125,126};  
Line(126) = {126,127};  
Line(127) = {127,128};  
Line(128) = {128,129};  
Line(129) = {129,130};  
Line(130) = {130,131};  
Line(131) = {131,132};  
Line(132) = {132,133};  
Line(133) = {133,134};  
Line(134) = {134,135};  
Line(135) = {135,136};  
Line(136) = {136,137};  
Line(137) = {137,138};  
Line(138) = {138,139};  
Line(139) = {139,140};  
Line(140) = {140,141};  
Line(141) = {141,142};  
Line(142) = {142,143};  
Line(143) = {143,144};  
Line(144) = {144,145};  
Line(145) = {145,146};  
Line(146) = {146,147};  
Line(147) = {147,148};  
Line(148) = {148,149};  
Line(149) = {149,150};  
Line(150) = {150,151};  
Line(151) = {151,152};  
Line(152) = {152,153};  
Line(153) = {153,154};  
Line(154) = {154,155};  
Line(155) = {155,156};  
Line(156) = {156,157};  
Line(157) = {157,158};  
Line(158) = {158,159};  
Line(159) = {159,160};  
Line(160) = {160,161};  
Line(161) = {161,162};  
Line(162) = {162,163};  
Line(163) = {163,164};  
Line(164) = {164,165};  
Line(165) = {165,166};  
Line(166) = {166,167};  
Line(167) = {167,168};  
Line(168) = {168,169};  
Line(169) = {169,170};  
Line(170) = {170,171};  
Line(171) = {171,172};  
Line(172) = {172,173};  
Line(173) = {173,174};  
Line(174) = {174,175};  
Line(175) = {175,176};  
Line(176) = {176,177};  
Line(177) = {177,178};  
Line(178) = {178,179};  
Line(179) = {179,180};  
Line(180) = {180,181};  
Line(181) = {181,182};  
Line(182) = {182,183};  
Line(183) = {183,184};  
Line(184) = {184,185};  
Line(185) = {185,186};  
Line(186) = {186,187};  
Line(187) = {187,188};  
Line(188) = {188,189};  
Line(189) = {189,190};  
Line(190) = {190,191};  
Line(191) = {191,192};  
Line(192) = {192,193};  
Line(193) = {193,194};  
Line(194) = {194,195};  
Line(195) = {195,196};  
Line(196) = {196,197};  
Line(197) = {197,198};  
Line(198) = {198,199};  
Line(199) = {199,200};  
Line(200) = {200,201};  
Line(201) = {201,202};  
Line(202) = {202,203};  
Line(203) = {203,204};  
Line(204) = {204,205};  
Line(205) = {205,206};  
Line(206) = {206,207};  
Line(207) = {207,208};  
Line(208) = {208,209};  
Line(209) = {209,210};  
Line(210) = {210,211};  
Line(211) = {211,212};  
Line(212) = {212,213};  
Line(213) = {213,214};  
Line(214) = {214,215};  
Line(215) = {215,216};  
Line(216) = {216,217};  
Line(217) = {217,218};  
Line(218) = {218,219};  
Line(219) = {219,220};  
Line(220) = {220,221};  
Line(221) = {221,222};  
Line(222) = {222,223};  
Line(223) = {223,224};  
Line(224) = {224,225};  
Line(225) = {225,226};  
Line(226) = {226,227};  
Line(227) = {227,228};  
Line(228) = {228,229};  
Line(229) = {229,230};  
Line(230) = {230,231};  
Line(231) = {231,232};  
Line(232) = {232,233};  
Line(233) = {233,234};  
Line(234) = {234,235};  
Line(235) = {235,236};  
Line(236) = {236,237};  
Line(237) = {237,238};  
Line(238) = {238,239};  
Line(239) = {239,240};  
Line(240) = {240,241};  
Line(241) = {241,242};  
Line(242) = {242,243};  
Line(243) = {243,244};  
Line(244) = {244,245};  
Line(245) = {245,246};  
Line(246) = {246,247};  
Line(247) = {247,248};  
Line(248) = {248,249};  
Line(249) = {249,250};  
Line(250) = {250,251};  
Line(251) = {251,252};  
Line(252) = {252,253};  
Line(253) = {253,254};  
Line(254) = {254,255};  
Line(255) = {255,256};  
Line(256) = {256,257};  
Line(257) = {257,258};  
Line(258) = {258,259};  
Line(259) = {259,260};  
Line(260) = {260,261};  
Line(261) = {261,262};  
Line(262) = {262,263};  
Line(263) = {263,264};  
Line(264) = {264,265};  
Line(265) = {265,266};  
Line(266) = {266,267};  
Line(267) = {267,268};  
Line(268) = {268,269};  
Line(269) = {269,270};  
Line(270) = {270,271};  
Line(271) = {271,272};  
Line(272) = {272,273};  
Line(273) = {273,274};  
Line(274) = {274,275};  
Line(275) = {275,276};  
Line(276) = {276,277};  
Line(277) = {277,278};  
Line(278) = {278,279};  
Line(279) = {279,280};  
Line(280) = {280,281};  
Line(281) = {281,282};  
Line(282) = {282,283};  
Line(283) = {283,284};  
Line(284) = {284,285};  
Line(285) = {285,286};  
Line(286) = {286,287};  
Line(287) = {287,288};  
Line(288) = {288,289};  
Line(289) = {289,290};  
Line(290) = {290,291};  
Line(291) = {291,292};  
Line(292) = {292,293};  
Line(293) = {293,294};  
Line(294) = {294,295};  
Line(295) = {295,296};  
Line(296) = {296,297};  
Line(297) = {297,298};  
Line(298) = {298,299};  
Line(299) = {299,300};  
Line(300) = {300,301};  
Line(301) = {301,302};  
Line(302) = {302,303};  
Line(303) = {303,304};  
Line(304) = {304,305};  
Line(305) = {305,306};  
Line(306) = {306,307};  
Line(307) = {307,308};  
Line(308) = {308,309};  
Line(309) = {309,310};  
Line(310) = {310,311};  
Line(311) = {311,312};  
Line(312) = {312,313};  
Line(313) = {313,314};  
Line(314) = {314,315};  
Line(315) = {315,316};  
Line(316) = {316,317};  
Line(317) = {317,318};  
Line(318) = {318,319};  
Line(319) = {319,320};  
Line(320) = {320,1};  
Line Loop(1) = {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320};  
Plane Surface(2) = {1};  
Physical Surface(99) = {2};  
//Physical Line(1) = {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320};

The erro:  
current line = 8  
Assertion fail : (area \> 0)  
line :301, in file ./include/fem.hpp  
Assertion fail : (area \> 0)  
line :301, in file ./include/fem.hpp  
err code 6 , mpirank 0