what was your command line (now I sound like Doug)? Including structurals from different days may not work as you may have large differential distortions due to differences in e.g. shimming, gradient nonlinearities, etc... that will preclude an accurate motion correction. Certainly it failed in this case.
cheers Bruce On Fri, 10 Aug 2012, Garikoitz Lerma Usabiaga wrote: > Thanks for the answer Bruce, > it is still running, so I killed the process. > > When using two individual structural images separately, the recon-all process > was OK. When I tried to use both structurals, I can check that the T1.mgz has > some strange distortions (please check image attached). > > > > > > When it is ok using two structurals (different days, same subject)? In this > is case, is there something we can do to fix it or should be use just one of > them? > > > Many thanks, > Gari > > > > On 2012-08-05, at 23:25, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > >> Hi Gari >> >> is it still running? The time it takes is square in the convex hull of the >> largest defect, so that can take a long time. A 45K defect is too big and >> typically means something is dramatically wrong, like the cerebellum or >> skull is attached. >> >> cheers >> Bruce >> >> >> On Sun, 5 Aug 2012, Garikoitz Lerma Usabiaga wrote: >> >>> Hi FS experts, I've run recon-all -i file -s subject -qcache -measure >>> thickness -all to: >>> - 18 subjects, session 1 T1 >>> - same 18 subjects, session 2 T1 >>> and everything went well. >>> Then I copied the <subject_id_session>/mri/orig/001.mgz-s to >>> <subject_id>/mri/orig/001.mgz and 002.mgz, and run the same command again: >>> recon-all -s <subject_id> -qcache -measure thickness -all >>> Half of the subjects are failing when trying to correct the topology. Please >>> find below the outputs of two of the subjects. >>> Should I use the -i and the original files instead of the already created >>> 001.mgz files? What should I check in order to avoid this error or what >>> should I do in order to correct it? >>> thank you very much, >>> Gari >>> ************************************************************* >>> INFO: assuming .mgz format >>> $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ >>> $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ >>> before topology correction, eno=-956 (nv=167898, nf=337708, ne=506562, >>> g=479) >>> 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 10 iterations >>> marking ambiguous vertices... >>> 127705 ambiguous faces found in tessellation >>> segmenting defects... >>> 125 defects found, arbitrating ambiguous regions... >>> analyzing neighboring defects... >>> -merging segment 6 into 1 >>> -merging segment 9 into 1 >>> -merging segment 21 into 1 >>> -merging segment 24 into 1 >>> -merging segment 26 into 1 >>> -merging segment 29 into 1 >>> -merging segment 44 into 1 >>> -merging segment 56 into 1 >>> -merging segment 2 into 1 >>> -merging segment 65 into 1 >>> -merging segment 67 into 1 >>> -merging segment 71 into 1 >>> -merging segment 4 into 1 >>> -merging segment 12 into 1 >>> -merging segment 34 into 18 >>> -merging segment 30 into 19 >>> -merging segment 38 into 35 >>> -merging segment 61 into 47 >>> -merging segment 107 into 106 >>> -merging segment 115 into 113 >>> 105 defects to be corrected >>> 0 vertices coincident >>> reading input surface >>> /home/BCBL/glerma/freesurfer/subjects/BERTSO/B_16/surf/lh.qsphere.nofix... >>> reading brain volume from brain... >>> reading wm segmentation from wm... >>> Computing Initial Surface Statistics >>> -face loglikelihood: -7.9838 (-3.9919) >>> -vertex loglikelihood: -5.7349 (-2.8674) >>> -normal dot loglikelihood: -3.5106 (-3.5106) >>> -quad curv loglikelihood: -6.1770 (-3.0885) >>> Total Loglikelihood : -23.4063 >>> CORRECTING DEFECT 0 (vertices=23, convex hull=21) >>> After retessellation of defect 0, euler #=-32 (96640,274187,177515) : >>> difference with theory (-102) = -70 >>> CORRECTING DEFECT 1 (vertices=44927, convex hull=14482) >>> Topology Correction Parametersretessellation 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 1.44 2010/05/27 23:37:16 nicks Exp $ >>> $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ >>> before topology correction, eno=-600 (nv=159708, nf=320616, ne=480924, >>> g=301) >>> 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 8 iterations >>> marking ambiguous vertices... >>> 115040 ambiguous faces found in tessellation >>> segmenting defects... >>> 96 defects found, arbitrating ambiguous regions... >>> analyzing neighboring defects... >>> -merging segment 16 into 0 >>> -merging segment 39 into 0 >>> -merging segment 48 into 0 >>> -merging segment 22 into 21 >>> -merging segment 38 into 34 >>> -merging segment 42 into 37 >>> -merging segment 70 into 69 >>> 89 defects to be corrected >>> 0 vertices coincident >>> reading input >>> surface/home/BCBL/glerma/freesurfer/subjects/BERTSO/B_11b/surf/lh.qsphere.nofix... >>> reading brain volume from brain... >>> reading wm segmentation from wm... >>> Computing Initial Surface Statistics >>> -face loglikelihood: -7.9998 (-3.9999) >>> -vertex loglikelihood: -5.5541 (-2.7771) >>> -normal dot loglikelihood: -3.5423 (-3.5423) >>> -quad curv loglikelihood: -6.1041 (-3.0520) >>> Total Loglikelihood : -23.2003 >>> CORRECTING DEFECT 0 (vertices=41794, convex hull=12626) >>> >> >> >> 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 . 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. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
