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Bug 2524 - ft_write_mri (nii output) incorrectly writes non 1mm isotropic data.

Reported 2014-04-03 17:16:00 +0200
Modified 2014-06-18 12:31:32 +0200
Product: FieldTrip
Component: external
Version: unspecified
Hardware: PC
Operating System: Linux
Importance: P5 normal
Assigned to: Jan-Mathijs Schoffelen
Depends on:
See also:

Luke - 2014-04-03 17:16:38 +0200

Created attachment 602 minimal example of bug. ft_write_mri fails to correctly set the pixel dimensions for non 1x1x1 mri data, when it uses MRIwrite.m. MRIwrite is the default when supplied with a nii file output, so this would effect any user not explicitly requesting 'dataformat' = 'nifti_spm' I would suggest that at a minimum the default be switched to nifti_spm, and the bug be sent upstream to the whom ever maintains this code. attached is quick minimal example... best, Luke

Robert Oostenveld - 2014-04-03 17:24:17 +0200

Hi Luke, thanks for reporting the bug and the details. @Jan-Mathijs, I suspect you have most expertise in the MRI writing stuff, can I assign this to you? Robert

Jan-Mathijs Schoffelen - 2014-04-03 19:48:57 +0200

bash-4.1$ svn commit -m "bugfix - added correct pixel dimensions when writing to nifti" fileio/ft_write_mri.m test/test_bug2524.m Sending fileio/ft_write_mri.m Adding test/test_bug2524.m Transmitting file data .. Committed revision 9343. Note to Robert: the test function has a system call to an fsl-function. It works for me, but I don't know whether fsl is standard on the path.