Hi Maria --
If there are holes/edges in the surface `mris_curvature_stats` it will
fail.
On Wed, 2019-07-24 at 10:03 +0200, Maria Kalemanov wrote:
> Hello FreeSurfer developers,
>
> I have three issues with mris_curvature_stats:
>
> 1. I attempted to compute curvature on a *noisy sphere* surface
> (attached) using different -a parameter values, integers from 0 to
> 10, like this:
>
> mris_curvature_stats -a 5 -f surface -m -o noisy_sphere_r10_a5.stats
> -G --signedPrincipals --writeCurvatureFiles noisy_sphere
> noisy_sphere_r10
>
> However, there is no slight difference between the curvatures in the
> output files. Also the runtimes do not vary. Am I calling the
> function wrong?
> Attached is also the ".stats" output in case it's of any use.
>
> 2. When running the same command as in 1. (without -a parameter) on a
> *noisy cylinder *surface (attached), I got the following standard
> output with errors:
>
> Outputting results using filestem [
> noisy_cylinder_r10_h25.stats ]
> Toggling save flag on curvature
> files [ ok ]
> Toggling 'signedPrincipals' flag
> ON [ ok ]
> Toggling save flag on curvature
> files [ ok ]
> Setting surface [
> noisy_cylinder/noisy_cylinder_r10_h25.surface ]
> Reading
> surface... [ ok ]
> Calculating Discrete Principal Curvatures...
> Determining geometric order for vertex faces...
> [#FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 94,
> faces = 4, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 106,
> faces = 4, packed = 2
> No such file or directory
> ##################FACES_aroundVertex_reorder: packed / faces
> mismatch; vertex = 1344, faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1346,
> faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1347,
> faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1348,
> faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1350,
> faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1351,
> faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1352,
> faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1354,
> faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1356,
> faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1389,
> faces = 4, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1393,
> faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1394,
> faces = 3, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1395,
> faces = 4, packed = 2
> No such file or directory
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1398,
> faces = 3, packed = 2
> No such file or directory
> #] [ ok ]
> FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1399,
> faces = 3, packed = 2
> Determining KH curvatures...
> [FACES_Hcurvature_determineSign: During call 2, the passed faces do
> not share an edge
>
>
> 3. When running the same command as in 1. (without -a parameter) on a
> *smooth cylinder* surface (attached), I got the following standard
> output with an error:
>
> Saving surf/smooth_cylinder_r10_h25.surface as a surface
> Outputting results using filestem [
> smooth_cylinder_r10_h25.stats ]
> Toggling save flag on curvature
> files [ ok ]
> Toggling 'signedPrincipals' flag
> ON [ ok ]
> Toggling save flag on curvature
> files [ ok ]
> Setting surface [
> smooth_cylinder/smooth_cylinder_r10_h25.surface ]
> Reading
> surface... [ ok ]
> Calculating Discrete Principal Curvatures...
> Determining geometric order for vertex faces...
> [run_freesurfer_curvature.sh: line 10: 24318 Segmentation
> fault (core dumped) mris_curvature_stats -f surface -m -o
> ${BASE}.stats -G --signedPrincipals --writeCurvatureFiles $SUBJECT
> $BASE
>
> I've searched the list and no similar errors have been reported. Does
> anyone know why the errors happen?
> Can it be because the cylinder surfaces are open and have edges?
>
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-
> v6.0.0-2beb96c
> 2) Platform: SUSE Linux Enterprise Server 12 SLES 12 SP 1
> 3) uname -a: Linux hpcl5004 3.12.74-60.64.40-default #1 SMP Wed May
> 10 05:07:16 UTC 2017 (4eb35ec) x86_64 x86_64 x86_64 GNU/Linux
>
> Thanks and best regards
> Maria
>
> External Email - Use Caution
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--
Rudolph Pienaar, M.Eng, Dr.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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