Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Error During Fix Topology and Brain Usability
by Angel Hammond 23 Dec '20

23 Dec '20

External Email - Use Caution 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

2 1

How to remove clusters less than 50 vertex/voxels in FreeSurfer during visualisation
by Sunil Khokhar 23 Dec '20

23 Dec '20

External Email - Use Caution Dear Experts! After doing the statistics I want to remove clusters that are less than 50 voxels/vertices from sig.mgh file which contains the visualisation of the results. Looking forward to your advices. Thanks in advance!

2 1

Recon-all error: MatrixMultiply: m1 is null!
by Boa Sorte Silva, Narlon 23 Dec '20

23 Dec '20

External Email - Use Caution Hi there, Hope this finds you well I have noticed the following error for some of my runs: @# Cortical ribbon mask Mon Dec 14 15:43:24 PST 2020 /Applications/freesurfer/7.1.1/subjects/BT_long/BT_055_base/mri \n mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --parallel BT_055_base \n SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long loading input data... Running hemis in parallel Processing left hemi Processing right hemi computing distance to right white surface computing distance to left white surface error: MatrixMultiply: m1 is null! Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020 Here are details of the computer and FS version I am using: * OS: macOS Mojave (10.14.4) * FS: 7.1.1 It seems to happen at random, whenever I run recon-all on the same subject again, the error doesn’t occur. This is true for cross-sectional, base, and long processing steps in my machine. I have seen an email relating to this issue before, but I wasn’t able to access the attachment file which would fix the problem. I was wondering if you guys would be able to help? Thank you Nárlon Cássio Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia Twitter: @BoaNarlon

2 1

asegstats2table
by Alberto Del Cerro Leon 23 Dec '20

23 Dec '20

External Email - Use Caution Hello Freesurfers, I have a question about the command asegstats2table. I want to obtain the structural data of a group set based on labels created by myself. I see that this is possible with mris_anatomicalstats for 1 subject but can I obtain the data for all my subjects in some way like asegstats2table using my labels?

3 3

group analyses
by Sara Lyn 23 Dec '20

23 Dec '20

External Email - Use Caution Hi FS developers, I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte carlo) for a surface based thickness group analysis. I am trying to extract volume measures from the same significant thickness ROIs. Is there any way to do this? Thank you! Sara

3 8

linkedUbuntu 18 virtual disk image - Developer password {Disarmed}
by C. Teurlings 23 Dec '20

23 Dec '20

1 0

Unable to unsubscribe {Disarmed}
by Snedden, Ali 23 Dec '20

23 Dec '20

External Email - Use Caution Hello, When I go to http://secure-web.cisco.com/1jgCpVnCnpYUf1STtrprTp2p1sr_-sFIyb-fzDa-XLhkXgR…, and go to “Freesurfer Subscribers” -> “Unsubscribe or edit options” and enter my email address and press the “Unsubscribe or edit options” button, I get a “The proxy server is refusing connections” Error. I see this (or similar message) in Firefox, Chrome and Safari. I’m on OSX 10.14.6. Ali

1 0

Trouble with mris_divide_parcellation
by Hyon, Justin J. 23 Dec '20

23 Dec '20

External Email - Use Caution I am having some trouble with mris_divide_parcellation. When I follow the procedure in —help, my input and output annotations appear to be identical. The input annotation consists of 5 labels that I’m trying to divide into either 2 or 3 regions. The output contains the exact same 5 regions. I am running the command from the home directory. I’m on OS X Catalina and Freesurfer 7.1.0. The input and output are below: $ mris_divide_parcellation EM rh reg_to_subdivide.annot path/to/splittable/rh_splittable.txt subdivided_regs reading colortable from annotation file... colortable with 76 entries read (originally ./EM/label/custom/aparc.annot.a2009s.ctab) interpreting 4th command line arg as split file name dividing G_front_middle (15) into 3 parts dividing G_front_sup (16) into 3 parts dividing G_orbital (24) into 2 parts dividing G_rectus (31) into 2 parts dividing S_front_sup (55) into 3 parts dividing S_pericallosal (67) into 2 parts allocating new colortable with 5 additional units... supposed to be reproducible but seed not set saving annotation to subdivided_regs I was wondering what I was doing wrong, and how I can make the function output an annot with subdivided labels?

1 0

convert .vtk to .annot
by 1248742467 23 Dec '20

23 Dec '20

External Email - Use Caution Hello, everyone I have lh.labels.DKT31.manual.vtk file, but I want to convert it to lh.labels.DKT31.manual.annot. Now, I use fs6 version, if you know please tell me! I also heard that convetr .vtk to .label then convert .label to .annot, just use mri_convert?

1 0

Superficial white matter surface reconstruction
by Gugger, James J 22 Dec '20

22 Dec '20

External Email - Use Caution Good morning, I am interested in reconstructing the superficial white matter surface (i.e., the surface 1 or 2 mm below the white surface). Can you give me some guidance on how to do this or find it if it is part of recon-all? Thank you, Jim Gugger James Gugger, MD, PharmD Instructor of Neurology University of Pennsylvania

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