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Bug 2939 - conflict in cfg.headshape.headshape & cfg.individual.headshape in ft_volumerealign & ft_interactiverealign respectively

Reported 2015-07-28 21:55:00 +0200
Modified 2019-08-10 12:31:16 +0200
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Linux
Importance: P5 normal
Assigned to:
Depends on:
See also:

Stephen Whitmarsh - 2015-07-28 21:55:52 +0200

Hi there buggers, Found my password... Anyway, here goes again: ft_volumerealign now expects the headshape struct in cfg.individual.headshape (or breaks on line 68). However, in my case its also calls ft_interactiverealign which expects cfg.headshape.headshape (line 509) which isn't passed through properly. At that point it is in cfg.headshape again. Its a bugger, no? All the best from the Swedish "summer". Hope its better wherever you are. Cheers, Stephen p.s. working on SVN rev 10561

Stephen Whitmarsh - 2015-07-28 22:27:37 +0200

NB: To be clear: ft_volumerealign calls ft_interactiveralign

Jan-Mathijs Schoffelen - 2015-07-29 08:22:12 +0200

Line 68 in my version of ft_volumerealign is in the middle of the documentation section of the function...

Stephen Whitmarsh - 2015-07-29 09:31:58 +0200

Ah sorry - other way around. Line 68(67) in ft_interactiverealign, 509 in ft_volumerealign.

Jan-Mathijs Schoffelen - 2015-07-29 09:35:10 +0200

Aha, that explains it. Looks like Robert's recent changes to accommodate the new naming convention (from 'vol' to 'headmodel') causes some problems. Do you happen to have some data and code to quickly reproduce this?

Stephen Whitmarsh - 2015-07-29 09:57:06 +0200

Thanks! Coming up - but server just crashed...

Stephen Whitmarsh - 2015-07-29 10:18:28 +0200

Created attachment 726 headshape

Stephen Whitmarsh - 2015-07-29 10:20:08 +0200

It crashes at the second call to ft_volumerealign. I attached the headshape. The MRI is too large to upload. Shall I send it to you (JM) by mail? Else you should be able to use any MRI, but then need to run through the first part. cfg = []; cfg.method = 'interactive'; cfg.coordsys = 'neuromag'; [mri_realigned] = ft_volumerealign(cfg, mri_orig); cfg = []; cfg.method = 'headshape'; cfg.headshape.headshape = shape; [mri_realigned] = ft_volumerealign(cfg, mri_realigned);

Jan-Mathijs Schoffelen - 2015-07-29 11:05:01 +0200

[jansch@mentat002 fieldtrip]$ svn commit -m "bugfix - fixed some incompatibilities after making the change in naming from vol to headmodel" ft_interactiverealign.m Sending ft_interactiverealign.m Transmitting file data . Committed revision 10562. [jansch@mentat002 fieldtrip]$ Hi Stephen, The calls to ft_checkconfig at the beginning in ft_interactiverealign caused the problem. I think I fixed it now.

Stephen Whitmarsh - 2015-07-29 11:17:40 +0200

It works! Held!

Robert Oostenveld - 2019-08-10 12:31:16 +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