Check the lh.orig and lh.inflated surfaces On 2/15/19 3:34 PM, ?? wrote: > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution > > For more than 3 hours > > ---Original--- > *From:* "Greve, Douglas N.,Ph.D."<dgr...@mgh.harvard.edu> > *Date:* Fri, Feb 15, 2019 20:03 PM > *To:* "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>; > *Subject:* Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc > > how long? > > On 2/15/19 2:49 PM, ?? wrote: >> >> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2 External Email - Use Caution >> >> Hi >> Thanks for your quickly reply, yes continue to run but not print more >> on terminal anymore. >> >> ---Original--- >> *From:* "Greve, Douglas N.,Ph.D."<dgr...@mgh.harvard.edu> >> *Date:* Fri, Feb 15, 2019 19:01 PM >> *To:* "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>; >> *Subject:* Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc >> >> Do you mean that it continues to run but does not do anything (eg, >> print more to the terminal) or that it has crashed? If it is hanging, >> how long? Nothing looks suspicious in the output. >> >> On 2/15/19 12:59 PM, ?? wrote: >>> >>> ?0?2?0?2?0?2?0?2?0?2 ?0?2 External Email - Use Caution >>> >>> Hi Greve, >>> i solved this problem, but had a new one with recon-all, when i run >>> the recon-all data, sometimes it hang in the very last step of the >>> recon-all. here is the related part of output in terminal. i have >>> attached the recon-all log and status log. Have a nice weekend! >>> cheers >>> >>> #@# Curv .H and .K rh Fri Feb 15 17:30:27 GMT 2019 >>> >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf >>> >>> \n mris_curvature -w rh.white.preaparc \n >>> >>> total integrated curvature = 11.983*4pi (150.582) --> -11 handles >>> >>> ICI = 180.5, FI = 1886.9, variation=29597.577 >>> >>> writing Gaussian curvature to >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.white.preaparc.K...done. >>> >>> writing mean curvature to >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.white.preaparc.H...done. >>> >>> rm -f rh.white.H >>> >>> ln -s rh.white.preaparc.H rh.white.H >>> >>> rm -f rh.white.K >>> >>> ln -s rh.white.preaparc.K rh.white.K >>> >>> \n mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 >>> rh.inflated \n >>> >>> normalizing curvature values. >>> >>> averaging curvature patterns 5 times. >>> >>> sampling 10 neighbors out to a distance of 10 mm >>> >>> 148 vertices thresholded to be in k1 ~ [-1.38 0.32], k2 ~ [-0.18 0.09] >>> >>> total integrated curvature = 0.554*4pi (6.968) --> 0 handles >>> >>> ICI = 1.3, FI = 8.1, variation=139.341 >>> >>> 115 vertices thresholded to be in [-0.05 0.02] >>> >>> writing Gaussian curvature to >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.inflated.K...thresholding >>> >>> curvature at 99.90% level >>> >>> curvature mean = 0.000, std = 0.001 >>> >>> 77 vertices thresholded to be in [-0.20 0.15] >>> >>> done. >>> >>> writing mean curvature to >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.inflated.H...curvature >>> >>> mean = -0.018, std = 0.022 >>> >>> done. >>> >>> \n#----------------------------------------- >>> >>> #@# Curvature Stats lh Fri Feb 15 17:31:32 GMT 2019 >>> >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf >>> >>> \n mris_curvature_stats -m --writeCurvatureFiles -G -o >>> ../stats/lh.curv.stats -F smoothwm subject lh curv sulc \n >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Toggling save flag on curvature files ?0?2 >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 ?0?2 [ ok ] >>> >>> Outputting results using filestem ?0?2 [ ../stats/lh.curv.stats ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Toggling save flag on curvature files ?0?2 >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 ?0?2 [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Setting surface?0?2 ?0?2 ?0?2 [ >>> subject/lh.smoothwm ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 Reading surface... ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Setting texture ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 ?0?2 ?0?2 [ curv ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 Reading texture... ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Setting texture ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 ?0?2 ?0?2 [ sulc ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 Reading texture...Gb_filter = 0 >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 Calculating Discrete Principal Curvatures... >>> >>> ?0?2 Determining geometric order for vertex faces... >>> [####################] [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Determining KH >>> curvatures... >>> [####################] [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Determining k1k2 >>> curvatures... >>> [####################] [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 deltaViolations?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 ?0?2 ?0?2 ?0?2 [ 213 ] >>> >>> Gb_filter = 0 >>> >>> >>> WARN:?0?2 ?0?2 S lookup ?0?2 min: -0.021311 >>> >>> WARN:?0?2 ?0?2 S explicit min: 0.000000 vertex = 907 >>> >>> \n#----------------------------------------- >>> >>> #@# Curvature Stats rh Fri Feb 15 17:31:38 GMT 2019 >>> >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf >>> >>> \n mris_curvature_stats -m --writeCurvatureFiles -G -o >>> ../stats/rh.curv.stats -F smoothwm subject rh curv sulc \n >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Toggling save flag on curvature files ?0?2 >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 ?0?2 [ ok ] >>> >>> Outputting results using filestem ?0?2 [ ../stats/rh.curv.stats ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Toggling save flag on curvature files ?0?2 >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 ?0?2 [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Setting surface?0?2 ?0?2 ?0?2 [ >>> subject/rh.smoothwm ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 Reading surface... ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Setting texture ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 ?0?2 ?0?2 [ curv ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 Reading texture... ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Setting texture ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 ?0?2 ?0?2 [ sulc ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 Reading texture...Gb_filter = 0 >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 Calculating Discrete Principal Curvatures... >>> >>> ?0?2 Determining geometric order for vertex faces... >>> [####################] [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Determining KH >>> curvatures... >>> [####################] [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 Determining k1k2 >>> curvatures... >>> [####################] [ ok ] >>> >>> ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 deltaViolations?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 >>> ?0?2 ?0?2 ?0?2 ?0?2 [ 257 ] >>> >>> Gb_filter = 0 >>> >>> >>> WARN:?0?2 ?0?2 S lookup ?0?2 min: -0.254695 >>> >>> WARN:?0?2 ?0?2 S explicit min: >>> >>> @# Sphere lh Fri Feb 15 17:31:44 GMT 2019 >>> >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/scripts >>> >>> \n mris_sphere -rusage >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/touch/rusage.mris_sphere.lh.dat >>> >>> -seed 1234 ../surf/lh.inflated ../surf/lh.sphere \n >>> >>> setting seed for random number genererator to 1234 >>> >>> $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ >>> >>> ?0?2 $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ >>> >>> reading original vertex positions... >>> >>> unfolding cortex into spherical form... >>> >>> surface projected - minimizing metric distortion... >>> >>> >>> == Number of threads available to mris_sphere for OpenMP = 1 == >>> >>> scaling brain by 0.321... >>> >>> MRISunfold() max_passes = 1 ------- >>> >>> tol=5.0e-01, sigma=0.0, host=cengz, nav=1024, nbrs=2, l_area=1.000, >>> l_dist=1.000 >>> >>> using quadratic fit line minimization >>> >>> complete_dist_mat 0 >>> >>> rms 0 >>> >>> smooth_averages 0 >>> >>> remove_neg 0 >>> >>> ico_order 0 >>> >>> which_surface 0 >>> >>> target_radius 0.000000 >>> >>> nfields 0 >>> >>> scale 1.000000 >>> >>> desired_rms_height -1.000000 >>> >>> momentum 0.900000 >>> >>> nbhd_size 7 >>> >>> max_nbrs 8 >>> >>> niterations 25 >>> >>> nsurfaces 0 >>> >>> SURFACES 3 >>> >>> flags 0 (0) >>> >>> use curv 0 >>> >>> no sulc 0 >>> >>> no rigid align 0 >>> >>> mris->nsize 2 >>> >>> mris->hemisphere 0 >>> >>> randomSeed 1234 >>> >>> >>> ------------------ Original ------------------ >>> *From: *?0?2"Greve, Douglas N.,Ph.D.";<dgr...@mgh.harvard.edu>; >>> *Send time:*?0?2Tuesday, Feb 12, 2019 0:41 AM >>> *To:* "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>; >>> *Subject: *?0?2Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc >>> >>> can you send the full mri_surf2surf terminal output? >>> >>> On 2/11/19 8:08 AM, ?? wrote: >>> > >>> > ?0?2?0?2?0?2?0?2?0?2 ?0?2 External Email - Use Caution >>> > >>> > Hello FreeSurfer Developers, >>> > >>> > I didn't cache the data during recon-all, so I ran the >>> > >>> > >?0?2?0?2?0?2 ?0?2 ?0?2 following: >>> > >>> > > >>> > >>> > >?0?2?0?2?0?2?0?2?0?2 ?0?2 ?0?2 ?0?2?0?2 ?0?2 mris_preproc ?Cfsgd >>> > >PDDvsHC.fsgd --target fsaverage >>> > >>> > >?0?2?0?2?0?2 ?0?2 ?0?2 --hemi lh >>> > >>> > >?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 ?0?2 ?0?2 --meas thickness >>> > >--out lh.MMSE-AD.thickness.00.mgh >>> > >>> > > >>> > >>> > >?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 ?0?2 ?0?2 It seemed to run >>> > >smoothly (I've attached the log >>> below) >>> > >>> > >?0?2?0?2?0?2 ?0?2 ?0?2 so I >>> > >>> > >?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 ?0?2 ?0?2 ran the next step: >>> > >>> > > >>> > >>> > >?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 ?0?2 ?0?2 mri_surf2surf --hemi >>> > >lh --s fsaverage --sval >>> > >>> > >?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 ?0?2 ?0?2 >>> > >lh.PDDvsHC.thickness.00.mgh --fwhm 10 --cortex --tval >>> > >>> > >?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 ?0?2 ?0?2 >>> > >lh.PDDvsHC.thickness.10.mgh >>> > >>> > > >>> > >>> > >?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 ?0?2 ?0?2 I got the following >>> > >error: >>> > >>> > > >>> > >>> > >?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 ?0?2 ?0?2 Reading source >>> > >surface reg >>> > >>> > > >>> > >>> > > freesurfer/subjects/fsaverage/surf/lh.sphere.reg >>> > >>> > >?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 ?0?2 ?0?2 Loading source data >>> > >>> > > >>> > >>> > > >>> > >>> > >>> mghRead(/Users/cengzhou/Desktop/volumetric_FS/FS/lh.PDDvsHC.thickness.00.mgh, >>> >>> >>> > -1): could not open file >>> > >>> > recon-all.log: see attached >>> > >>> > Platform: mac os 10 >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> > 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 >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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