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Dear Experts,
I have a brain that I have been getting an error for during fix topology during recon-all using Freesurfer 6.0 on macOS Catalina. I have read a couple of threads on this same kind of error on the Freesurfer list and it seems this is due to some error in wm segmentation, cerebellum, or skull. However, being new with Freesurfer I am not sure what to check and how to fix such a large defect (or if it's even worth fixing - is this usable?). Just a few notes on this scan, it has heavy motion and was flagged by our radiologist as having 'excessive white matter changes'. I uploaded the subject to the FTP named '088.tar.gz' to take a look at. Thank you!
The recon-all.log error message here:
INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-788 (nv=159056, nf=319688, ne=479532, g=395) using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 101024 ambiguous faces found in tessellation segmenting defects... 166 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 8 into 3 -merging segment 14 into 3 -merging segment 48 into 3 -merging segment 7 into 4 -merging segment 6 into 5 -merging segment 1 into 10 -merging segment 20 into 16 -merging segment 19 into 18 -merging segment 10 into 23 -merging segment 32 into 29 -merging segment 37 into 30 -merging segment 75 into 45 -merging segment 62 into 64 -merging segment 109 into 92 -merging segment 127 into 92 -merging segment 128 into 92 -merging segment 141 into 92 -merging segment 159 into 92 -merging segment 157 into 92 -merging segment 125 into 121 -merging segment 123 into 122 -merging segment 139 into 133 144 defects to be corrected 0 vertices coincident reading input surface /study3/midus3/data/freesurfer/subjects/088/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4365 (-4.7182) -vertex loglikelihood: -6.8975 (-3.4488) -normal dot loglikelihood: -3.5115 (-3.5115) -quad curv loglikelihood: -6.1828 (-3.0914) Total Loglikelihood : -26.0283
CORRECTING DEFECT 0 (vertices=115, convex hull=128, v0=113) After retessellation of defect 0 (v0=113), euler #=-112 (102634,295350,192604) : difference with theory (-141) = -29
CORRECTING DEFECT 1 (vertices=43, convex hull=79, v0=2438) After retessellation of defect 1 (v0=2438), euler #=-111 (102656,295448,192681) : difference with theory (-140) = -29
CORRECTING DEFECT 2 (vertices=3335, convex hull=1683, v0=2597) XL defect detected... After retessellation of defect 2 (v0=2597), euler #=-113 (103831,299911,195967) : difference with theory (-139) = -26
CORRECTING DEFECT 3 (vertices=108, convex hull=48, v0=2938) After retessellation of defect 3 (v0=2938), euler #=-111 (103837,299955,196007) : difference with theory (-138) = -27
CORRECTING DEFECT 4 (vertices=1336, convex hull=711, v0=3387) XL defect detected... After retessellation of defect 4 (v0=3387), euler #=-109 (104350,301857,197398) : difference with theory (-137) = -28
CORRECTING DEFECT 5 (vertices=162, convex hull=218, v0=4667) After retessellation of defect 5 (v0=4667), euler #=-108 (104432,302198,197658) : difference with theory (-136) = -28
CORRECTING DEFECT 6 (vertices=18, convex hull=48, v0=5608) After retessellation of defect 6 (v0=5608), euler #=-107 (104444,302251,197700) : difference with theory (-135) = -28
CORRECTING DEFECT 7 (vertices=562, convex hull=419, v0=5682) L defect detected... After retessellation of defect 7 (v0=5682), euler #=-106 (104704,303262,198452) : difference with theory (-134) = -28
CORRECTING DEFECT 8 (vertices=44, convex hull=101, v0=5705) After retessellation of defect 8 (v0=5705), euler #=-105 (104716,303339,198518) : difference with theory (-133) = -28
CORRECTING DEFECT 9 (vertices=37, convex hull=38, v0=8189) After retessellation of defect 9 (v0=8189), euler #=-104 (104719,303364,198541) : difference with theory (-132) = -28
CORRECTING DEFECT 10 (vertices=180, convex hull=169, v0=8978) After retessellation of defect 10 (v0=8978), euler #=-103 (104772,303609,198734) : difference with theory (-131) = -28
CORRECTING DEFECT 11 (vertices=12, convex hull=25, v0=9633) After retessellation of defect 11 (v0=9633), euler #=-102 (104774,303621,198745) : difference with theory (-130) = -28
CORRECTING DEFECT 12 (vertices=243, convex hull=275, v0=9655) After retessellation of defect 12 (v0=9655), euler #=-100 (104899,304141,199142) : difference with theory (-129) = -29
CORRECTING DEFECT 13 (vertices=223, convex hull=157, v0=12134) After retessellation of defect 13 (v0=12134), euler #=-99 (104986,304474,199389) : difference with theory (-128) = -29
CORRECTING DEFECT 14 (vertices=27, convex hull=65, v0=12681) After retessellation of defect 14 (v0=12681), euler #=-98 (104995,304521,199428) : difference with theory (-127) = -29
CORRECTING DEFECT 15 (vertices=914, convex hull=491, v0=12900) L defect detected... After retessellation of defect 15 (v0=12900), euler #=-96 (105241,305518,200181) : difference with theory (-126) = -30
CORRECTING DEFECT 16 (vertices=85, convex hull=105, v0=13658) After retessellation of defect 16 (v0=13658), euler #=-95 (105291,305713,200327) : difference with theory (-125) = -30
CORRECTING DEFECT 17 (vertices=53, convex hull=86, v0=14037) After retessellation of defect 17 (v0=14037), euler #=-94 (105321,305842,200427) : difference with theory (-124) = -30
CORRECTING DEFECT 18 (vertices=255, convex hull=132, v0=14332) After retessellation of defect 18 (v0=14332), euler #=-93 (105393,306128,200642) : difference with theory (-123) = -30
CORRECTING DEFECT 19 (vertices=38, convex hull=80, v0=17657) After retessellation of defect 19 (v0=17657), euler #=-92 (105417,306235,200726) : difference with theory (-122) = -30
CORRECTING DEFECT 20 (vertices=8, convex hull=28, v0=17757) After retessellation of defect 20 (v0=17757), euler #=-91 (105418,306249,200740) : difference with theory (-121) = -30
CORRECTING DEFECT 21 (vertices=538, convex hull=333, v0=18109) After retessellation of defect 21 (v0=18109), euler #=-89 (105554,306832,201189) : difference with theory (-120) = -31
CORRECTING DEFECT 22 (vertices=262, convex hull=253, v0=18458) After retessellation of defect 22 (v0=18458), euler #=-87 (105680,307339,201572) : difference with theory (-119) = -32
CORRECTING DEFECT 23 (vertices=7, convex hull=32, v0=20614) After retessellation of defect 23 (v0=20614), euler #=-86 (105681,307353,201586) : difference with theory (-118) = -32
CORRECTING DEFECT 24 (vertices=36, convex hull=55, v0=20986) After retessellation of defect 24 (v0=20986), euler #=-85 (105689,307400,201626) : difference with theory (-117) = -32
CORRECTING DEFECT 25 (vertices=1348, convex hull=596, v0=21154) XL defect detected... After retessellation of defect 25 (v0=21154), euler #=-84 (106133,309038,202821) : difference with theory (-116) = -32
CORRECTING DEFECT 26 (vertices=59, convex hull=109, v0=24677) After retessellation of defect 26 (v0=24677), euler #=-83 (106173,309205,202949) : difference with theory (-115) = -32
CORRECTING DEFECT 27 (vertices=18, convex hull=22, v0=26139) After retessellation of defect 27 (v0=26139), euler #=-82 (106173,309212,202957) : difference with theory (-114) = -32
CORRECTING DEFECT 28 (vertices=22, convex hull=15, v0=28505) After retessellation of defect 28 (v0=28505), euler #=-81 (106175,309222,202966) : difference with theory (-113) = -32
CORRECTING DEFECT 29 (vertices=47, convex hull=33, v0=28568) After retessellation of defect 29 (v0=28568), euler #=-80 (106179,309245,202986) : difference with theory (-112) = -32
CORRECTING DEFECT 30 (vertices=33, convex hull=68, v0=29152) After retessellation of defect 30 (v0=29152), euler #=-79 (106199,309331,203053) : difference with theory (-111) = -32
CORRECTING DEFECT 31 (vertices=23, convex hull=31, v0=29620) After retessellation of defect 31 (v0=29620), euler #=-78 (106200,309346,203068) : difference with theory (-110) = -32
CORRECTING DEFECT 32 (vertices=36, convex hull=69, v0=29653) After retessellation of defect 32 (v0=29653), euler #=-77 (106213,309410,203120) : difference with theory (-109) = -32
CORRECTING DEFECT 33 (vertices=32, convex hull=69, v0=30231) After retessellation of defect 33 (v0=30231), euler #=-76 (106232,309497,203189) : difference with theory (-108) = -32
CORRECTING DEFECT 34 (vertices=26, convex hull=69, v0=31159) After retessellation of defect 34 (v0=31159), euler #=-75 (106240,309544,203229) : difference with theory (-107) = -32
CORRECTING DEFECT 35 (vertices=1193, convex hull=611, v0=33216) XL defect detected... After retessellation of defect 35 (v0=33216), euler #=-73 (106607,310974,204294) : difference with theory (-106) = -33
CORRECTING DEFECT 36 (vertices=25, convex hull=54, v0=33352) After retessellation of defect 36 (v0=33352), euler #=-72 (106621,311037,204344) : difference with theory (-105) = -33
CORRECTING DEFECT 37 (vertices=106, convex hull=128, v0=33930) After retessellation of defect 37 (v0=33930), euler #=-71 (106682,311280,204527) : difference with theory (-104) = -33
CORRECTING DEFECT 38 (vertices=47, convex hull=35, v0=35396) After retessellation of defect 38 (v0=35396), euler #=-70 (106688,311309,204551) : difference with theory (-103) = -33
CORRECTING DEFECT 39 (vertices=88, convex hull=39, v0=35775) After retessellation of defect 39 (v0=35775), euler #=-69 (106697,311351,204585) : difference with theory (-102) = -33
CORRECTING DEFECT 40 (vertices=45, convex hull=21, v0=36715) After retessellation of defect 40 (v0=36715), euler #=-68 (106697,311358,204593) : difference with theory (-101) = -33
CORRECTING DEFECT 41 (vertices=83, convex hull=81, v0=36730) After retessellation of defect 41 (v0=36730), euler #=-68 (106724,311487,204695) : difference with theory (-100) = -32
CORRECTING DEFECT 42 (vertices=35, convex hull=75, v0=37712) After retessellation of defect 42 (v0=37712), euler #=-67 (106741,311570,204762) : difference with theory (-99) = -32
CORRECTING DEFECT 43 (vertices=66, convex hull=96, v0=38608) After retessellation of defect 43 (v0=38608), euler #=-66 (106780,311725,204879) : difference with theory (-98) = -32
CORRECTING DEFECT 44 (vertices=59, convex hull=35, v0=42853) After retessellation of defect 44 (v0=42853), euler #=-65 (106784,311748,204899) : difference with theory (-97) = -32
CORRECTING DEFECT 45 (vertices=31, convex hull=68, v0=43693) After retessellation of defect 45 (v0=43693), euler #=-64 (106800,311817,204953) : difference with theory (-96) = -32
CORRECTING DEFECT 46 (vertices=100, convex hull=159, v0=44412) After retessellation of defect 46 (v0=44412), euler #=-63 (106860,312071,205148) : difference with theory (-95) = -32
CORRECTING DEFECT 47 (vertices=2008, convex hull=765, v0=44793) XL defect detected... After retessellation of defect 47 (v0=44793), euler #=-63 (107570,314609,206976) : difference with theory (-94) = -31
CORRECTING DEFECT 48 (vertices=21, convex hull=63, v0=45597) After retessellation of defect 48 (v0=45597), euler #=-62 (107584,314672,207026) : difference with theory (-93) = -31
CORRECTING DEFECT 49 (vertices=5, convex hull=9, v0=46164) After retessellation of defect 49 (v0=46164), euler #=-61 (107585,314677,207031) : difference with theory (-92) = -31
CORRECTING DEFECT 50 (vertices=141, convex hull=53, v0=46378) After retessellation of defect 50 (v0=46378), euler #=-60 (107603,314756,207093) : difference with theory (-91) = -31
CORRECTING DEFECT 51 (vertices=89, convex hull=130, v0=47463) After retessellation of defect 51 (v0=47463), euler #=-59 (107666,315008,207283) : difference with theory (-90) = -31
CORRECTING DEFECT 52 (vertices=99, convex hull=86, v0=48729) After retessellation of defect 52 (v0=48729), euler #=-57 (107690,315116,207369) : difference with theory (-89) = -32
CORRECTING DEFECT 53 (vertices=23, convex hull=53, v0=49690) After retessellation of defect 53 (v0=49690), euler #=-56 (107701,315168,207411) : difference with theory (-88) = -32
CORRECTING DEFECT 54 (vertices=28, convex hull=61, v0=51301) After retessellation of defect 54 (v0=51301), euler #=-55 (107719,315249,207475) : difference with theory (-87) = -32
CORRECTING DEFECT 55 (vertices=10, convex hull=21, v0=53334) After retessellation of defect 55 (v0=53334), euler #=-54 (107721,315261,207486) : difference with theory (-86) = -32
CORRECTING DEFECT 56 (vertices=53, convex hull=85, v0=54650) After retessellation of defect 56 (v0=54650), euler #=-53 (107740,315353,207560) : difference with theory (-85) = -32
CORRECTING DEFECT 57 (vertices=65, convex hull=27, v0=58847) After retessellation of defect 57 (v0=58847), euler #=-52 (107744,315372,207576) : difference with theory (-84) = -32
CORRECTING DEFECT 58 (vertices=20, convex hull=32, v0=59115) After retessellation of defect 58 (v0=59115), euler #=-51 (107747,315391,207593) : difference with theory (-83) = -32
CORRECTING DEFECT 59 (vertices=41, convex hull=73, v0=60478) After retessellation of defect 59 (v0=60478), euler #=-50 (107763,315466,207653) : difference with theory (-82) = -32
CORRECTING DEFECT 60 (vertices=356, convex hull=211, v0=61182) After retessellation of defect 60 (v0=61182), euler #=-49 (107897,315966,208020) : difference with theory (-81) = -32
CORRECTING DEFECT 61 (vertices=8, convex hull=18, v0=61319) After retessellation of defect 61 (v0=61319), euler #=-48 (107898,315975,208029) : difference with theory (-80) = -32
CORRECTING DEFECT 62 (vertices=44, convex hull=71, v0=61429) After retessellation of defect 62 (v0=61429), euler #=-47 (107921,316072,208104) : difference with theory (-79) = -32
CORRECTING DEFECT 63 (vertices=29, convex hull=56, v0=63923) After retessellation of defect 63 (v0=63923), euler #=-46 (107936,316142,208160) : difference with theory (-78) = -32
CORRECTING DEFECT 64 (vertices=22, convex hull=36, v0=64851) After retessellation of defect 64 (v0=64851), euler #=-45 (107943,316174,208186) : difference with theory (-77) = -32
CORRECTING DEFECT 65 (vertices=156, convex hull=196, v0=65023) After retessellation of defect 65 (v0=65023), euler #=-44 (108028,316519,208447) : difference with theory (-76) = -32
CORRECTING DEFECT 66 (vertices=43, convex hull=50, v0=65760) After retessellation of defect 66 (v0=65760), euler #=-43 (108043,316582,208496) : difference with theory (-75) = -32
CORRECTING DEFECT 67 (vertices=46, convex hull=29, v0=67556) After retessellation of defect 67 (v0=67556), euler #=-42 (108048,316605,208515) : difference with theory (-74) = -32
CORRECTING DEFECT 68 (vertices=68, convex hull=85, v0=67614) After retessellation of defect 68 (v0=67614), euler #=-41 (108076,316725,208608) : difference with theory (-73) = -32
CORRECTING DEFECT 69 (vertices=232, convex hull=165, v0=69771) After retessellation of defect 69 (v0=69771), euler #=-41 (108175,317105,208889) : difference with theory (-72) = -31
CORRECTING DEFECT 70 (vertices=391, convex hull=190, v0=70249) After retessellation of defect 70 (v0=70249), euler #=-40 (108275,317488,209173) : difference with theory (-71) = -31
CORRECTING DEFECT 71 (vertices=24, convex hull=32, v0=70287) After retessellation of defect 71 (v0=70287), euler #=-39 (108279,317507,209189) : difference with theory (-70) = -31
CORRECTING DEFECT 72 (vertices=32, convex hull=53, v0=71355) After retessellation of defect 72 (v0=71355), euler #=-38 (108285,317547,209224) : difference with theory (-69) = -31
CORRECTING DEFECT 73 (vertices=178, convex hull=148, v0=72699) After retessellation of defect 73 (v0=72699), euler #=-37 (108302,317664,209325) : difference with theory (-68) = -31
CORRECTING DEFECT 74 (vertices=7, convex hull=30, v0=72932) After retessellation of defect 74 (v0=72932), euler #=-36 (108304,317678,209338) : difference with theory (-67) = -31
CORRECTING DEFECT 75 (vertices=177, convex hull=117, v0=73659) After retessellation of defect 75 (v0=73659), euler #=-35 (108386,317978,209557) : difference with theory (-66) = -31
CORRECTING DEFECT 76 (vertices=24, convex hull=56, v0=74392) After retessellation of defect 76 (v0=74392), euler #=-34 (108400,318044,209610) : difference with theory (-65) = -31
CORRECTING DEFECT 77 (vertices=26, convex hull=51, v0=74882) After retessellation of defect 77 (v0=74882), euler #=-33 (108409,318088,209646) : difference with theory (-64) = -31
CORRECTING DEFECT 78 (vertices=203, convex hull=159, v0=76388) After retessellation of defect 78 (v0=76388), euler #=-32 (108491,318401,209878) : difference with theory (-63) = -31
CORRECTING DEFECT 79 (vertices=30159, convex hull=7767, v0=78672) Segmentation fault (core dumped) Linux c139.keck.waisman.wisc.edu 3.10.0-1127.19.1.el7.x86_64 #1 SMP Thu Aug 20 14:39:03 CDT 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 088 exited with ERRORS at Sat Nov 7 18:24:33 CST 2020
Angel Hammond
Research Specialist
Center for Healthy Minds
University of Wisconsin-Madison