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For more than 3 hours
---Original--- From: "Greve, Douglas N.,Ph.D."DGREVE@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, 妮 wrote:
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, 妮 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, 妮 wrote:
External Email - Use CautionHello FreeSurfer Developers,
I didn't cache the data during recon-all, so I ran the
following:mris_preproc –fsgd PDDvsHC.fsgd --target fsaverage--hemi lh--meas thickness --out lh.MMSE-AD.thickness.00.mghIt seemed to run smoothly (I've attached the log below)so Iran the next step:mri_surf2surf --hemi lh --s fsaverage --svallh.PDDvsHC.thickness.00.mgh --fwhm 10 --cortex --tvallh.PDDvsHC.thickness.10.mghI got the following error:Reading source surface regfreesurfer/subjects/fsaverage/surf/lh.sphere.regLoading source datamghRead(/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
Check the lh.orig and lh.inflated surfaces
On 2/15/19 3:34 PM, 妮 wrote:
External Email - Use Caution
For more than 3 hours
---Original--- *From:* "Greve, Douglas N.,Ph.D."DGREVE@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, 妮 wrote:
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, 妮 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, 妮 wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I didn't cache the data during recon-all, so I ran the
following:
mris_preproc –fsgd 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
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@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
妮