mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in volmue.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.PDDvsHC.volume.10.mgh

 mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir lh.volume.PDDvsHC.glimdir --eres-save

 mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces

We I check the results, it still talked about the cortical thickness , so could you tell me how to change this commends to the volume of subcortical. Or do you have the example which use GLM for comparing the difference of subcortical volume between two groups.

Thanks so much for your help

Yours

Zeng

Here is the results

        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."<DGREVE@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, ÄÝ wrote:

        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 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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