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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 AM
To: "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>;
Subject:  Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc

can 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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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