I think you are right, the auto skull stripping probably didn't quite do the job. We are working on trying to skull strip the dicoms manually before starting over again. In the meantime, I uploaded the lh-inflated (that seems to be the only one in the subjects/[SUBJECT]/surf/ folder). Thanks
On Thu, Feb 28, 2013 at 9:44 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Eli > > I think that defect is simply too big (it would take forever to fix). It's > more than half of the size of a typical cortical hemisphere model. Did you > check the skull stripping? And send us images (medial and lateral) of the > ?h.inflated.nofix in tksurfer > > cheers > Bruce > > > On Thu, 28 Feb 2013, Eli Fredman wrote: > > Hi all, >> I have been trying to run freesurfer on a case for awhile now. After >> receiving multiple errors when using the skull stripped nifti (nii.gz) >> file, >> I tried to use the original dicoms as the input. While I haven't run into >> any errors, the process seems to have frozen at "CORRECTING DEFECT 41 >> (vertices=89913, convex hull=4452)". Any help would be greatly >> appreciated. >> Thanks, >> Eli >> >> ========== >> >> INFO: assuming .mgz format >> $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ >> before topology correction, eno=-380 (nv=211494, nf=423748, ne=635622, >> g=191) >> 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 12 iterations >> marking ambiguous vertices... >> 188325 ambiguous faces found in tessellation >> segmenting defects... >> 55 defects found, arbitrating ambiguous regions... >> analyzing neighboring defects... >> -merging segment 11 into 10 >> -merging segment 15 into 13 >> -merging segment 18 into 14 >> -merging segment 24 into 17 >> -merging segment 36 into 23 >> -merging segment 38 into 23 >> -merging segment 31 into 29 >> -merging segment 39 into 33 >> -merging segment 46 into 45 >> -merging segment 0 into 51 >> 45 defects to be corrected >> 0 vertices coincident >> reading input surface/projects/schiz/ra/eli/**freesurfer5.1/subjects/** >> 002dicoms/surf/lh.qsphere.nof >> ix... >> reading brain volume from brain... >> reading wm segmentation from wm... >> Computing Initial Surface Statistics >> -face loglikelihood: -9.0381 (-4.5191) >> -vertex loglikelihood: -5.9029 (-2.9514) >> -normal dot loglikelihood: -3.5586 (-3.5586) >> -quad curv loglikelihood: -5.9424 (-2.9712) >> Total Loglikelihood : -24.4420 >> >> CORRECTING DEFECT 0 (vertices=82, convex hull=99) >> After retessellation of defect 0, euler #=-22 (115136,340924,225766) : >> difference with theory (-42) = -20 >> >> CORRECTING DEFECT 1 (vertices=33, convex hull=78) >> After retessellation of defect 1, euler #=-21 (115149,340994,225824) : >> difference with theory (-41) = -20 >> >> CORRECTING DEFECT 2 (vertices=33, convex hull=68) >> After retessellation of defect 2, euler #=-20 (115168,341086,225898) : >> difference with theory (-40) = -20 >> >> CORRECTING DEFECT 3 (vertices=101, convex hull=114) >> After retessellation of defect 3, euler #=-19 (115213,341271,226039) : >> difference with theory (-39) = -20 >> >> CORRECTING DEFECT 4 (vertices=128, convex hull=124) >> After retessellation of defect 4, euler #=-18 (115250,341441,226173) : >> difference with theory (-38) = -20 >> >> CORRECTING DEFECT 5 (vertices=24, convex hull=54) >> After retessellation of defect 5, euler #=-17 (115262,341498,226219) : >> difference with theory (-37) = -20 >> >> CORRECTING DEFECT 6 (vertices=26, convex hull=57) >> After retessellation of defect 6, euler #=-16 (115271,341549,226262) : >> difference with theory (-36) = -20 >> >> CORRECTING DEFECT 7 (vertices=571, convex hull=248) >> After retessellation of defect 7, euler #=-15 (115423,342130,226692) : >> difference with theory (-35) = -20 >> >> CORRECTING DEFECT 8 (vertices=380, convex hull=194) >> After retessellation of defect 8, euler #=-14 (115506,342478,226958) : >> difference with theory (-34) = -20 >> >> CORRECTING DEFECT 9 (vertices=993, convex hull=488) >> After retessellation of defect 9, euler #=-15 (115632,343151,227504) : >> difference with theory (-33) = -18 >> >> CORRECTING DEFECT 10 (vertices=92, convex hull=56) >> After retessellation of defect 10, euler #=-14 (115642,343197,227541) : >> difference with theory (-32) = -18 >> >> CORRECTING DEFECT 11 (vertices=245, convex hull=137) >> After retessellation of defect 11, euler #=-12 (115687,343396,227697) : >> difference with theory (-31) = -19 >> >> CORRECTING DEFECT 12 (vertices=42, convex hull=87) >> After retessellation of defect 12, euler #=-10 (115704,343479,227765) : >> difference with theory (-30) = -20 >> >> CORRECTING DEFECT 13 (vertices=105, convex hull=48) >> After retessellation of defect 13, euler #=-10 (115716,343539,227813) : >> difference with theory (-29) = -19 >> >> CORRECTING DEFECT 14 (vertices=172, convex hull=170) >> After retessellation of defect 14, euler #=-8 (115780,343817,228029) : >> difference with theory (-28) = -20 >> >> CORRECTING DEFECT 15 (vertices=5, convex hull=31) >> After retessellation of defect 15, euler #=-7 (115781,343828,228040) : >> difference with theory (-27) = -20 >> >> CORRECTING DEFECT 16 (vertices=9, convex hull=28) >> After retessellation of defect 16, euler #=-6 (115784,343843,228053) : >> difference with theory (-26) = -20 >> >> CORRECTING DEFECT 17 (vertices=33, convex hull=61) >> After retessellation of defect 17, euler #=-5 (115799,343912,228108) : >> difference with theory (-25) = -20 >> >> CORRECTING DEFECT 18 (vertices=19, convex hull=36) >> Warning - incorrect dp selected!!!!(-97.779794 >= -97.779795 ) >> After retessellation of defect 18, euler #=-4 (115800,343927,228123) : >> difference with theory (-24) = -20 >> >> CORRECTING DEFECT 19 (vertices=2147, convex hull=849) >> After retessellation of defect 19, euler #=-3 (116319,345967,229645) : >> difference with theory (-23) = -20 >> >> CORRECTING DEFECT 20 (vertices=6, convex hull=25) >> After retessellation of defect 20, euler #=-2 (116320,345976,229654) : >> difference with theory (-22) = -20 >> >> CORRECTING DEFECT 21 (vertices=40, convex hull=54) >> After retessellation of defect 21, euler #=-1 (116337,346050,229712) : >> difference with theory (-21) = -20 >> >> CORRECTING DEFECT 22 (vertices=5, convex hull=28) >> Warning - incorrect dp selected!!!!(-60.449796 >= -60.449800 ) >> After retessellation of defect 22, euler #=0 (116339,346063,229724) : >> difference with theory (-20) = -20 >> >> CORRECTING DEFECT 23 (vertices=28, convex hull=68) >> After retessellation of defect 23, euler #=1 (116348,346118,229771) : >> difference with theory (-19) = -20 >> >> CORRECTING DEFECT 24 (vertices=55, convex hull=89) >> After retessellation of defect 24, euler #=3 (116361,346191,229833) : >> difference with theory (-18) = -21 >> >> CORRECTING DEFECT 25 (vertices=7, convex hull=24) >> After retessellation of defect 25, euler #=4 (116364,346206,229846) : >> difference with theory (-17) = -21 >> >> CORRECTING DEFECT 26 (vertices=34, convex hull=61) >> After retessellation of defect 26, euler #=5 (116377,346272,229900) : >> difference with theory (-16) = -21 >> >> CORRECTING DEFECT 27 (vertices=220, convex hull=226) >> After retessellation of defect 27, euler #=6 (116428,346544,230122) : >> difference with theory (-15) = -21 >> >> CORRECTING DEFECT 28 (vertices=116, convex hull=73) >> After retessellation of defect 28, euler #=6 (116438,346608,230176) : >> difference with theory (-14) = -20 >> >> CORRECTING DEFECT 29 (vertices=87, convex hull=115) >> After retessellation of defect 29, euler #=7 (116474,346762,230295) : >> difference with theory (-13) = -20 >> >> CORRECTING DEFECT 30 (vertices=5, convex hull=36) >> Warning - incorrect dp selected!!!!(-57.697888 >= -57.697893 ) >> After retessellation of defect 30, euler #=8 (116476,346776,230308) : >> difference with theory (-12) = -20 >> >> CORRECTING DEFECT 31 (vertices=6, convex hull=22) >> After retessellation of defect 31, euler #=9 (116478,346787,230318) : >> difference with theory (-11) = -20 >> >> CORRECTING DEFECT 32 (vertices=34, convex hull=26) >> After retessellation of defect 32, euler #=10 (116483,346809,230336) : >> difference with theory (-10) = -20 >> >> CORRECTING DEFECT 33 (vertices=292, convex hull=113) >> After retessellation of defect 33, euler #=11 (116504,346932,230439) : >> difference with theory (-9) = -20 >> >> CORRECTING DEFECT 34 (vertices=22, convex hull=70) >> After retessellation of defect 34, euler #=12 (116515,346990,230487) : >> difference with theory (-8) = -20 >> >> CORRECTING DEFECT 35 (vertices=6, convex hull=19) >> After retessellation of defect 35, euler #=13 (116517,347003,230499) : >> difference with theory (-7) = -20 >> >> CORRECTING DEFECT 36 (vertices=10, convex hull=48) >> After retessellation of defect 36, euler #=15 (116521,347034,230528) : >> difference with theory (-6) = -21 >> >> CORRECTING DEFECT 37 (vertices=5, convex hull=28) >> After retessellation of defect 37, euler #=16 (116522,347046,230540) : >> difference with theory (-5) = -21 >> >> CORRECTING DEFECT 38 (vertices=39, convex hull=93) >> After retessellation of defect 38, euler #=17 (116545,347155,230627) : >> difference with theory (-4) = -21 >> >> CORRECTING DEFECT 39 (vertices=20, convex hull=30) >> After retessellation of defect 39, euler #=18 (116549,347178,230647) : >> difference with theory (-3) = -21 >> >> CORRECTING DEFECT 40 (vertices=26, convex hull=52) >> After retessellation of defect 40, euler #=19 (116560,347231,230690) : >> difference with theory (-2) = -21 >> >> CORRECTING DEFECT 41 (vertices=89913, convex hull=4452) >> >> >> >> -- >> Eli Fredman, BA >> Research Assistant >> Psychiatry Neuroimaging Laboratory >> Harvard Medical School, Brigham and Women's Hospital >> 1249 Boylston St, 3rd Floor >> Boston, MA 02215 >> Office: (617) 525-6118 >> Cell: (314) 952-8098 >> Fax: (617) 525-6150 >> > -- Eli Fredman, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6118 Cell: (314) 952-8098 Fax: (617) 525-6150
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