External Email - Use Caution
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
Toggling save flag on curvature files [ ok ]
Outputting results using filestem [ ../stats/lh.curv.stats ]
Toggling save flag on curvature files [ ok ]
Setting surface [ subject/lh.smoothwm ]
Reading surface... [ ok ]
Setting texture [ curv ]
Reading texture... [ ok ]
Setting texture [ sulc ]
Reading texture...Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vertex faces... [####################] [ ok ]
Determining KH curvatures... [####################] [ ok ]
Determining k1k2 curvatures... [####################] [ ok ]
deltaViolations [ 213 ]
Gb_filter = 0
WARN: S lookup min: -0.021311
WARN: 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
Toggling save flag on curvature files [ ok ]
Outputting results using filestem [ ../stats/rh.curv.stats ]
Toggling save flag on curvature files [ ok ]
Setting surface [ subject/rh.smoothwm ]
Reading surface... [ ok ]
Setting texture [ curv ]
Reading texture... [ ok ]
Setting texture [ sulc ]
Reading texture...Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vertex faces... [####################] [ ok ]
Determining KH curvatures... [####################] [ ok ]
Determining k1k2 curvatures... [####################] [ ok ]
deltaViolations [ 257 ]
Gb_filter = 0
WARN: S lookup min: -0.254695
WARN: 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 $
$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: "Greve, Douglas N.,Ph.D.";<DGREVE@mgh.harvard.edu>;Send time: Tuesday, Feb 12, 2019 0:41 AMSubject: Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproccan you send the full mri_surf2surf terminal output?
On 2/11/19 8:08 AM, ÄÝ wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I didn't cache the data during recon-all, so I ran the
>
> > following:
>
> >
>
> > mris_preproc ¨Cfsgd PDDvsHC.fsgd --target fsaverage
>
> > --hemi lh
>
> > --meas thickness --out lh.MMSE-AD.thickness.00.mgh
>
> >
>
> > It seemed to run smoothly (I've attached the log below)
>
> > so I
>
> > ran the next step:
>
> >
>
> > mri_surf2surf --hemi lh --s fsaverage --sval
>
> > lh.PDDvsHC.thickness.00.mgh --fwhm 10 --cortex --tval
>
> > lh.PDDvsHC.thickness.10.mgh
>
> >
>
> > I got the following error:
>
> >
>
> > Reading source surface reg
>
> >
>
> > freesurfer/subjects/fsaverage/surf/lh.sphere.reg
>
> > 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
>
>
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