External Email - Use Caution
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
Hi Marina
can you upload this subject? I'm not sure what is going on. Or send us the recon-all.log?
The vertex error means that the surfaces don't match. This usually means that you recreated some but not all of the surfaces for one of the hemis
cheers Bruce
On Thu, 28 May 2020, Marina Fernández wrote:
External Email - Use Caution
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Marina Fernández