hmmm, maybe the nonlinearities between days are too big for the registration.
Bruce On Sun, 12 Aug 2012, Garikoitz Lerma Usabiaga wrote: > Many thanks Bruce, > I will choose the best one in this case. > > The command line was: > recon-all -s B_06 -qcache -measure thickness -all > (I already had copied by hand the /mri/orig/001.mgz and 002.mgz) > > Just in case I repeated the process with the original files, but I had > exactly the same results. This was the command line: > recon-all -i > /home/glerma/glerma/freesurfer/subjects/BERTSO_MRI/BS3_06/58153751 -i > /home/glerma/glerma/freesurfer/subjects/BERTSO_MRI/SESION2/06_BERTSOLARI_IEA/54336388 > -s B_06c -qcache -measure thickness -all > > > thanks! > Gari > > > On 2012-08-10, at 19:05, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > >> 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. 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