Hi Milène
a couple of things. First, to view a surface in freeview you have to specify that it is a surface with -f before the surface file name. So, from the mri dir you could do:
freeview -v norm.mgz -f ../surf/lh.orig.nofix ../surf/lh.inflated.nofix
Second, how long did you wait? Big defects take a long time. You should definitely look at your inflated and orig surfaces though to make sure that some dramatic isn't wrong (like skull attached, or hemispheres not separated) as your defect is probably too large to be an ordinary one that the topo fixer will correct successfully.
cheers Bruce
On Wed, 13 Feb 2019, "Milene Bürger" wrote:
External Email - Use Caution
Hi Freesurfers, I tried to run the recon-all command for several subjects of my study. It worked out for all of them except for one. This one froze at fixing topology „Correcting defect“ 11 out of 140 defects. I looked for advises in the mailing list but I can’t find any major problems in the images that Freesurfer processed so far. The last correct file that I can open in freeview, is filled.mgz (the skull and cerebellum are properly removed and it shows the two hemispheres with 127 for rh and 255 for lh). I can’t find the file "filled-pretess255.mgz“ which should be the output, but I do have the files lh.orig.nofix and rh.orig.nofix for example. I tried to look at these files, but freeview can't open them (failed to load MRI) so that I can’t see if there are topological defects to correct as you described on one of the FsTutorials. I already tried to run only the autorecon2 command, but the same freezing problem appeared at one point. I also tried to only use the mri_pretess command with different options, but it didn’t work. I copied you the fix topology and what I tried with mri_pretess. I use freesurfer version 6.0.1. Thanks a lot! Milène mris_fix_topology -rusage/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versu ch_Pretess/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -g 1234 FJ_20170425_T1_Versuch_Pretess lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234
Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0
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=-666 (nv=184736, nf=370804, ne=556206, g=334) 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... 92297 ambiguous faces found in tessellation segmenting defects... 151 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 3 into 2 -merging segment 32 into 12 -merging segment 94 into 12 -merging segment 45 into 36 -merging segment 53 into 37 -merging segment 62 into 60 -merging segment 81 into 70 -merging segment 88 into 70 -merging segment 144 into 132 -merging segment 141 into 138 -merging segment 150 into 147 140 defects to be corrected 0 vertices coincident reading input surface/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versu ch_Pretess/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3516 (-4.6758) -vertex loglikelihood: -6.1930 (-3.0965) -normal dot loglikelihood: -3.5442 (-3.5442) -quad curv loglikelihood: -6.0556 (-3.0278) Total Loglikelihood : -25.1443 CORRECTING DEFECT 0 (vertices=9329, convex hull=1902, v0=235) XL defect detected... After retessellation of defect 0 (v0=235), euler #=-122 (135106,396534,261306) : difference with theory (-137) = -15 CORRECTING DEFECT 1 (vertices=47, convex hull=87, v0=788) After retessellation of defect 1 (v0=788), euler #=-121 (135129,396640,261390) : difference with theory (-136) = -15 CORRECTING DEFECT 2 (vertices=1438, convex hull=465, v0=1311) XL defect detected... After retessellation of defect 2 (v0=1311), euler #=-119 (135552,398142,262471) : difference with theory (-135) = -16 CORRECTING DEFECT 3 (vertices=24, convex hull=64, v0=9358) After retessellation of defect 3 (v0=9358), euler #=-118 (135563,398202,262521) : difference with theory (-134) = -16 CORRECTING DEFECT 4 (vertices=35, convex hull=54, v0=11845) After retessellation of defect 4 (v0=11845), euler #=-117 (135574,398251,262560) : difference with theory (-133) = -16 CORRECTING DEFECT 5 (vertices=68, convex hull=94, v0=12131) After retessellation of defect 5 (v0=12131), euler #=-116 (135584,398327,262627) : difference with theory (-132) = -16 CORRECTING DEFECT 6 (vertices=66, convex hull=29, v0=12470) After retessellation of defect 6 (v0=12470), euler #=-115 (135586,398344,262643) : difference with theory (-131) = -16 CORRECTING DEFECT 7 (vertices=29, convex hull=34, v0=16888) After retessellation of defect 7 (v0=16888), euler #=-114 (135587,398360,262659) : difference with theory (-130) = -16 CORRECTING DEFECT 8 (vertices=66, convex hull=79, v0=16899) After retessellation of defect 8 (v0=16899), euler #=-113 (135625,398509,262771) : difference with theory (-129) = -16 CORRECTING DEFECT 9 (vertices=219, convex hull=64, v0=16932) After retessellation of defect 9 (v0=16932), euler #=-112 (135644,398592,262836) : difference with theory (-128) = -16 CORRECTING DEFECT 10 (vertices=69, convex hull=58, v0=19570) After retessellation of defect 10 (v0=19570), euler #=-111 (135659,398659,262889) : difference with theory (-127) = -16 CORRECTING DEFECT 11 (vertices=18978, convex hull=4487, v0=19837) mri_pretess: mbuerger@beo-05:/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_2 0170425_T1/mri $ rm/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versu ch_Pretess/scripts/IsRunning.lh+rh rm: remove regular file`/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Vers uch_Pretess/scripts/IsRunning.lh+rh'? mbuerger@beo-05:/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_2 0170425_T1/mri $ mri_pretess -keep wm.mgz wm127 norm.mgz wm.mgz keeping edits Ambiguous edge configurations... Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 0 (out of 16189883: 0.000000) Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done