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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