Re: [Freesurfer] mri_curvature_stats: -a parameter has no effect and errors (FACES_aroundVertex_reorder: packed / faces mismatch, and Segmentation fault)

2019-07-30 Thread Maria Kalemanov 
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




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Re: [Freesurfer] mri_curvature_stats: -a parameter has no effect and errors (FACES_aroundVertex_reorder: packed / faces mismatch and Segmentation fault)

2019-07-29 Thread Maria Kalemanov 
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 Prin