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Bug 2928 - ft_volumesegment fails on 2015a

Reported 2015-07-14 16:59:00 +0200
Modified 2019-08-10 12:40:35 +0200
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P5 normal
Assigned to: Robert Oostenveld
Depends on:
See also:

Robert Oostenveld - 2015-07-14 16:59:11 +0200

Tjeerd wrote: Bij het analyseren van de MRI data gaat het mis en sluit Matlab (Matlab encountered an internal problem and needs to close). Ik heb het op twee computers getest en bij beide crashed Matlab. Het gaat om deze analyse: cfg = []; cfg.output = {'brain', 'skull', 'scalp'}; mri_segmented = ft_volumesegment(cfg, mri_resliced); De output die ik krijg: Converting the coordinate system from neuromag to spm Rescaling NIFTI: slope = 0.00342945, intercept = 0 Smoothing by 0 & 8mm.. Coarse Affine Registration.. Fine Affine Registration.. performing the segmentation on the specified volume creating scalpmask smoothing anatomy with a 5-voxel FWHM kernel thresholding anatomy at a relative threshold of 0.100 En dan crashed Matlab..

Robert Oostenveld - 2015-07-14 17:50:33 +0200

I was NOT able to reproduce the problem with R2015a on 64 bit linux.

Robert Oostenveld - 2015-07-14 18:00:31 +0200

roboos@mentat001> svn commit Adding test/test_bug2928.m Transmitting file data . Committed revision 10535. This is what is in the test script. The fiducial locations were determined interactively (there are some nice fat markers). ------------------------------------ filename = dccnpath('/home/common/matlab/fieldtrip/data/test/bug2928/e889.dcm'); mi = ft_read_mri(filename); cfg = []; cfg.coordsys = 'neuromag'; cfg.method = 'fiducial'; cfg.fidicial.nas = [39 135 88]; cfg.fidicial.lpa = [128 168 161]; cfg.fidicial.rpa = [128 164 15]; mri_realigned = ft_volumerealign(cfg, mri); cfg = []; seg = ft_volumesegment(cfg, mri_realigned); % THIS IS WHERE IT SUPPOSEDLY CRASHES cfg = []; cfg.funparameter = 'white'; ft_sourceplot(cfg, seg); ------------------------------------

Robert Oostenveld - 2015-07-16 16:18:55 +0200

I updated the test script a bit. I also had Tjeerd on Skype, and right now suspect that the problem is due to an SPM8 mex file that does not work properly on his OS X 10.10.4 computer. @Guillaume (CC), do you perhaps know of reported incompatibilities between SPM8 mex files and the latest OS X version?

Guillaume - 2015-07-16 20:13:28 +0200

(In reply to Robert Oostenveld from comment #3) I'm not aware of any but most MEX files in SPM8 were compiled with OS X 10.5.6 so you might try to recompile them first before investigating further.

Robert Oostenveld - 2017-10-03 11:17:30 +0200

this is an old issue, and seemed an external mex file problem. Nothing to be fixed in FT itself. Hence I'll close it.

Robert Oostenveld - 2019-08-10 12:34:24 +0200

This closes a whole series of bugs that have been resolved (either FIXED/WONTFIX/INVALID) for quite some time. If you disagree, please file a new issue on

Robert Oostenveld - 2019-08-10 12:40:35 +0200

This closes a whole series of bugs that have been resolved (either FIXED/WONTFIX/INVALID) for quite some time. If you disagree, please file a new issue on