Back to the main page.

Bug 1297 - error at ft_volumesegment

Reported 2012-01-30 17:22:00 +0100
Modified 2012-10-14 16:41:03 +0200
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Windows
Importance: P3 normal
Assigned to: Lilla Magyari
Depends on:
See also:

Lilla Magyari - 2012-01-30 17:22:17 +0100

hi, When I was running ft_volumesegment, I got an error: cfg = []; cfg.coordsys = 'spm'; cfg.output = {'skullstrip' 'brain'}; seg2 = ft_volumesegment(cfg, mri_nom); the input is volume data with dimensions [256 256 256] Warning: adding W:\fieldtrip-20120125\fieldtrip-20120125\external\spm8 toolbox to your Matlab path Warning: Could not get change notification handle for remote W:\fieldtrip-20120125\fieldtrip-20120125\external\spm8\@nifti\private. Windows has exhausted its pool of handles for this file server. Type 'help changeNotification' for more info. > In path at 110 In addpath at 87 In ft_hastoolbox>myaddpath at 376 In ft_hastoolbox at 311 In ft_volumesegment at 154 performing the segmentation on the specified volume ??? Out of memory. Type HELP MEMORY for your options. Error in ==> flipdim at 38 y = x(v{:}); Error in ==> ft_volumesegment at 408 segment.anatomy = flipdim(segment.anatomy, k); You can get mri_nom if you read in (ft_read_mri the orig-nomask.mgz volume in /home/language/lilmag/grandaverage_mne). thanks for help. Lilla

Eelke Spaak - 2012-01-30 17:39:23 +0100

Hi Lilla, it sounds like matlab was out of memory. What type of machine were you working on?

Robert Oostenveld - 2012-01-30 17:47:50 +0100

I created a test script with the actual data (test_bug1297) and copied the data to home/common. The test script does not reproduce the problem, it runs fine and reports having used 702MB of RAM for the computation.

Boris Reuderink - 2012-02-03 11:42:05 +0100

Lilla, how much memory do you have? Can you run the "memory" command in MATLAB?

Roemer van der Meij - 2012-05-16 13:19:47 +0200

Lilla, do you think this is still a problem, and if not, just close the bug? JM (not Roemer)

Lilla Magyari - 2012-10-14 16:41:03 +0200

I think also it is not a problem anymore.