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 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

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