Hi Bruce,
The talairach transform is reasonable and the aseg segment the cc correctly.
I run with freesurfer dev version the same command (recon all -autorecon-2wm -subjid post_006) and now I have more information about what could be the problem. The output of the terminal (that you can see below) says that there is a vertex in the curv file of each hemisphere that has one vertex number that it is not expected. When I open the curv file in tksurfer there is a 0 in these positions.
Maybe this output can be useful to help me solve the problem.
What do you think I should do? Thanks in advance!
mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated
setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
128 vertices thresholded to be in k1 ~ [-0.27 0.70], k2 ~ [-0.10 0.11]
total integrated curvature = 0.637*4pi (8.002) --> 0 handles
ICI = 1.5, FI = 8.0, variation=142.940
106 vertices thresholded to be in [-0.03 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
125 vertices thresholded to be in [-0.16 0.23]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.023
done.
@#@FSTIME 2020:05:28:10:21:34 mris_curvature N 12 e 52.03 S 0.20 U 51.78 P 99% M 334852 F 0 R 89611 W 0 c 174 w 1 I 0 O 1888 L 2.00 2.00 1.76
@#@FSLOADPOST 2020:05:28:10:22:26 mris_curvature N 12 2.00 2.00 1.77
#-----------------------------------------
#@# Curvature Stats lh Thu May 28 10:22:26 CEST 2020
/usr/local/freesurfer/subjects/post_006/surf
mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm post_006 lh curv sulc
Toggling save flag on curvature files [ ok ]
Outputting results using filestem [ ../stats/lh.curv.stats ]
Toggling save flag on curvature files [ ok ]
Setting surface [ post_006/lh.smoothwm ]
Reading surface... [ ok ]
Setting texture [ curv ]
Reading texture...error: No such file or directory
error: MRISreadNewCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/post_006/surf/lh.curv
***WARNING!***
Some error has occurred while reading 'lh.curv'.
This might be due a vertex incompatibility
between the surface 'lh.smoothwm' and curv 'lh.curv'.
You might be able to correct this by re-running
'mris_make_surfaces' on this dataset.
Skipping this (and any remaining) curvature files.
Any measurements / calcuations that depend on the
curvature file will be skipped.
*************
Calculating Discrete Principal Curvatures...
Determining geometric order for vno faces... [####################] [ ok ]
Determining KH curvatures... [####################] [ ok ]
Determining k1k2 curvatures... [####################] [ ok ]
deltaViolations [ 208 ]
WARN: S lookup min: -0.238596
WARN: S explicit min: 0.000000 vertex = 1525
@#@FSTIME 2020:05:28:10:22:26 mris_curvature_stats N 11 e 2.95 S 0.14 U 2.79 P 99% M 170736 F 6 R 48708 W 0 c 56 w 7 I 1104 O 7584 L 2.00 2.00 1.77
@#@FSLOADPOST 2020:05:28:10:22:29 mris_curvature_stats N 11 2.00 2.00 1.77
#-----------------------------------------
#@# Curvature Stats rh Thu May 28 10:22:29 CEST 2020
/usr/local/freesurfer/subjects/post_006/surf
mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm post_006 rh curv sulc
Toggling save flag on curvature files [ ok ]
Outputting results using filestem [ ../stats/rh.curv.stats ]
Toggling save flag on curvature files [ ok ]
Setting surface [ post_006/rh.smoothwm ]
Reading surface... [ ok ]
Setting texture [ curv ]
Reading texture...error: No such file or directory
error: MRISreadNewCurvature: incompatible vertex number in file /usr/local/freesurfer/subjects/post_006/surf/rh.curv
***WARNING!***
Some error has occurred while reading 'rh.curv'.
This might be due a vertex incompatibility
between the surface 'rh.smoothwm' and curv 'rh.curv'.
You might be able to correct this by re-running
'mris_make_surfaces' on this dataset.
Skipping this (and any remaining) curvature files.
Any measurements / calcuations that depend on the
curvature file will be skipped.
*************
Calculating Discrete Principal Curvatures...
Determining geometric order for vno faces... [####################] [ ok ]
Determining KH curvatures... [####################] [ ok ]
Determining k1k2 curvatures... [####################] [ ok ]
deltaViolations [ 190 ]
WARN: S lookup min: -0.040471
WARN: S explicit min: 0.000000 vertex = 53