Re: [Freesurfer] mri_curvature_stats: -a parameter has no effect and errors (FACES_aroundVertex_reorder: packed / faces mismatch, and Segmentation fault)
Dear Rudolph, Thanks a lot for your reply! Do you know why does it fail on holes/edges? Does the algorithm require each triangle vertex to have 1-ring neighbours? Also, do you by chance know how to use the -a parameter correctly? I did not observe any difference nor in the results nor in runtime with a call like this: mris_curvature_stats -a 5 -f surface -m -o noisy_sphere_r10_a5.stats -G --signedPrincipals --writeCurvatureFiles noisy_sphere noisy_sphere_r10 Many thanks and best wishes Maria On 30.07.19 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: > Hi Maria -- > > If there are holes/edges in the surface `mris_curvature_stats` it will > fail. -- Maria Kalemanov, M.Sc. PhD student Department Molecular Structural Biology Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany Phone:+49 89 8578-2041 signature.asc Description: OpenPGP digital signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_curvature_stats: -a parameter has no effect and errors (FACES_aroundVertex_reorder: packed / faces mismatch and Segmentation fault)
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
Re: [Freesurfer] mri_curvature_stats: -a parameter has no effect and errors (FACES_aroundVertex_reorder: packed / faces mismatch and Segmentation fault)
Dear Freesurfers,
Can anyone please help me with mris_curvature_stats? Anyone was using or
testing it and encountered the same parameter problem or errors?
Thanks and best
Maria
On 24.07.19 10:03, 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
