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 fischl@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 fischl@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)
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