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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer