Hi Bruce and Louis, Thank you for the suggestions. I will try them out.
Just fyi. For our dataset this error is very rare. So far it occured only in 1 out of 525+ scans processed with FS 5.1. Thank you, Mehul On Tue, Nov 1, 2011 at 6:50 AM, Louis Nicholas Vinke < vi...@nmr.mgh.harvard.edu> wrote: > Hi Mehul, > Alternatively you can try rerunning the skullstrip step, sometimes this > works as well. > > recon-all -skullstrip -autorecon2 -autorecon3 -s [SubjID] > > -Louis > > > On Tue, 1 Nov 2011, Bruce Fischl wrote: > > Hi Mehul >> >> this is a bug in the topology correction that we haven't been able to >> track down, mainly because the person who wrote this piece is long gone. If >> you edit the wm to remove a defect it usually goes away >> >> >> Bruce >> On Mon, 31 Oct 2011, Mehul Sampat wrote: >> >> Hi Folks >>> >>> I am using Freesurfer 5.1 and I get the following error: "ERROR: >>> _FindFacePath: could not find path!" >>> >>> Is this is a memory related issue ? The same case went through smoothly >>> with >>> Freesurfer 5.0. >>> Also I have not seen this error over a large number of subjects and I >>> thought it might be system related, >>> but even when I re-run it, I get the same error. >>> >>> From the recon-all.error file, the last command is "mris_topo_fixer -mgz >>> -warnings -seed 1234 ms0709_01 rh" >>> >>> Here is a small snippet from the recon-all.log file (just before the >>> error) >>> >>> Correcting Topology of defect 28 with euler number -1 (1 loops) >>> computing statistics for defect 28: 288 vertices >>> location: [ (106,175,134) - average intensity = 89.717 ] >>> -gray ( 85.29 , 6.61 ) -white ( 95.96 , 3.49 ) >>> -gray ( 83.95 , 18.89 ) -white ( 98.95 , 17.00 ) >>> -intensity (85.286896 [log = -2.118856 ]- 95.961853 [log = >>> -2.118159 >>> ] ) >>> -curv (k1=-0.131 (0.556) , r1 = 7.623 | k2=-0.051 (0.131), r2 = >>> 19.605 >>> ) >>> -curv (k1=-0.105 (0.609) , r1 = 9.520 | k2=-0.023 (0.212), r2 = >>> 42.735 >>> ) >>> max face = 548(548) - loop = 1 (1) - ntries = [83,229] >>> >>> BEST FITNESS (o)is -6.78736 >>> mri =0.000 curv = 1.594 unmri = 0.410 >>> ( f=0.00 , v=0.00 , c=1.59 , q= 3.19 ) >>> ( f=0.00 , v=0.00 , c=1.59 , q= 3.19 ) >>> >>> BEST FITNESS (M) is -6.40381 >>> mri =0.000 curv = 2.115 unmri = -2.054 >>> ( f=0.00 , v=0.00 , c=2.11 , q= 4.23 ) >>> ( f=0.00 , v=0.00 , c=2.11 , q= 4.23 ) >>> >>> ERROR: _FindFacePath: could not find path! >>> >>> Thanks >>> Mehul >>> >>> On Wed, Oct 26, 2011 at 6:03 PM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi >>> >>> you probably ran out of memory. That's a giant defect so >>> something is >>> badly wrong. Check to make sure that the hemis are separated and >>> that the >>> skull and cerebellum aren't attached >>> Bruce >>> On Wed, 26 Oct 2011, Sindhuja Tirumalai >>> Govindarajan wrote: >>> >>> > Hi all, >>> > > I got the following error while running recon-all on a patient >>> dataset. >>> > Kindly let me know how to proceed. >>> > > Thanks! >>> > Sindhuja >>> > > > Correction of the Topology >>> > Finding true center and radius of Spherical Surface...done >>> > Surface centered at (0,0,0) with radius 100.0 in 13 iterations >>> > marking ambiguous vertices... >>> > 129422 ambiguous faces found in tessellation >>> > segmenting defects... >>> > 51 defects found, arbitrating ambiguous regions... >>> > analyzing neighboring defects... >>> > -merging segment 1 into 0 >>> > -merging segment 2 into 0 >>> > -merging segment 8 into 0 >>> > -merging segment 5 into 7 >>> > -merging segment 28 into 12 >>> > -merging segment 35 into 31 >>> > -merging segment 47 into 43 >>> > 44 defects to be corrected >>> > 0 vertices coincident >>> > reading input surface >>> > /autofs/cluster/mscat/users/**caterina/3T/recons-04082011/** >>> MS_pt20_recon/surf/ >>> lh.qsphere.nofix... >>> > reading brain volume from brain... >>> > reading wm segmentation from wm... >>> > Computing Initial Surface Statistics >>> > -face loglikelihood: -9.5482 (-4.7741) >>> > -vertex loglikelihood: -6.9824 (-3.4912) >>> > -normal dot loglikelihood: -3.5307 (-3.5307) >>> > -quad curv loglikelihood: -5.9945 (-2.9973) >>> > Total Loglikelihood : -26.0558 >>> > > CORRECTING DEFECT 0 (vertices=50712, convex hull=8198) >>> > Segmentation fault >>> > > recon-all -s MS_pt20_recon exited with ERRORS at Wed Oct 26 18:49:31 >>> EDT 2011 >>> > > ______________________________**_________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> > >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> > > > ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> >>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >>> If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender >>> and properly >>> dispose of the e-mail. >>> >>> >>> >>> >>>
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