Hello, We have a case where -autorecon2 completed successfully, yet the right surface appears to have a topological defect. We discovered this because we got the following message upon trying to run 'mris_volume' on the pial surface:
--- mris_volume: surface rh.pial has an incorrect topology (eno=1) ---
Here is the output of mris_euler_number on that surface:
--- euler # = v-e+f = 2g-2: 133519 - 400551 + 267033 = 1 --> 1 holes F =2V-4: 267033 != 267038-4 (1) 2E=3F: 801102 != 801099 (3)
total defect index = 4 ---
Below I've appended the final lines from the log file of the Fix Topology stage (FS v3.0.5).
I've also attached two jpgs of the likely problem -- note the small black spot on the inflated surface, and the break of the orig and white surfaces in the medial temporal region of the tkmedit snapshot. (There is a small break in the pial surface as well, but it is hard to see in the jpg).
Should we just try running the Topology Fixer again? What should we try in order to get a correct topology for this surface?
thanks, Mike H.
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CORRECTING DEFECT 35 (vertices=61, convex hull=108) After retessellation of defect 35, euler #=-4 (133456,400244,266784) : difference with theory (-2) = 2
CORRECTING DEFECT 36 (vertices=86, convex hull=119) After retessellation of defect 36, euler #=-2 (133489,400394,266903) : difference with theory (-1) = 1
CORRECTING DEFECT 37 (vertices=9, convex hull=34) After retessellation of defect 37, euler #=-1 (133494,400421,266926) : difference with theory (0) = 1
CORRECTING DEFECT 38 (vertices=136, convex hull=61) After retessellation of defect 38, euler #=0 (133507,400486,266979) : difference with theory (1) = 1
CORRECTING DEFECT 39 (vertices=32, convex hull=74) After retessellation of defect 39, euler #=1 (133519,400551,267033) : difference with theory (2) = 1 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.04-->6.15) (max @ vno 133750 --> 134053) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.04-->6.15) (max @ vno 133750 --> 134053) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 120 mutations (34.1%), 232 crossovers (65.9%), 195 vertices were eliminated building final representation... 3035 vertices and 0 faces have been removed from triangulation after topology correction, eno=1 (nv=133519, nf=267033, ne=400551, g=0) writing corrected surface to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/011228_12436/surf/rh.orig... edge (34451<-->132983) has one single face 264775 ! edge (34451<-->132972) has one single face 264857 ! edge (132972<-->34451) has one single face 264857 ! edge (132972<-->132983) has one single face 264959 ! edge (132983<-->34451) has one single face 264775 ! edge (132983<-->132972) has one single face 264959 !
0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 59.9 minutes reading input surface /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/011228_12436/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... edge 34451 <--> 133998 has 1 face(s)! (264775) 133827 34451 133998 !!! edge 34451 <--> 133986 has 1 face(s)! (264857) 133909 133986 34451 !!! edge 133986 <--> 133998 has 1 face(s)! (264959) 133986 133992 133998 !!! 3 defective edges removing intersecting faces 000: 269 intersecting 001: 48 intersecting 002: 24 intersecting 003: 20 intersecting 004: 24 intersecting 005: 14 intersecting 006: 3 intersecting /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/011228_12436/scripts
mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
intersection removal took 0.02 hours removing intersecting faces 000: 202 intersecting 001: 43 intersecting 002: 20 intersecting expanding nbhd size to 2 003: 20 intersecting 004: 18 intersecting 005: 12 intersecting 006: 3 intersecting writing corrected surface to ../surf/rh.orig
rm ../surf/rh.inflated
