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Bug 1945 - create function that allows for manual editing of boolean volumes...

Reported 2013-01-23 11:55:00 +0100
Modified 2015-07-15 13:31:27 +0200
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P3 normal
Assigned to: Jan-Mathijs Schoffelen
Depends on:
See also:

Jan-Mathijs Schoffelen - 2013-01-23 11:55:43 +0100 improve segmentation results. this may be useful in the freesurfer pipeline; e.g. to remove strips of dura that keep attached to the segmented brain, and would avoid having to go to tkmedit or so. I will implement this in a private function volumeedit, along the lines of volumesmooth, volumethreshold, and volumefillholes

Jan-Mathijs Schoffelen - 2013-01-23 12:00:30 +0100

bash-3.2$ cd private bash-3.2$ svn add volumeedit.m A volumeedit.m bash-3.2$ svn commit -m "enhancement - first implementation, not called from a higher level function yet" volumeedit.m Adding volumeedit.m Transmitting file data . Committed revision 7373.

Jan-Mathijs Schoffelen - 2013-01-23 16:12:38 +0100

The question is now where to implement a call to this function. I'd vote for an implementation in ft_volumesegment.

Lilla Magyari - 2013-01-24 15:18:28 +0100

(In reply to comment #2) I think that would be cool. Perhaps ft_volumesegment could have options like cfg.method = 'manual', cfg.method = 'spm' and other (e.g. 'fsl' if the fsl bet is going to be implemented). lilla

Robert Oostenveld - 2013-01-24 16:40:35 +0100

(In reply to comment #3) I believe ft_prepare_mesh has a manual variant as well. Please have a look there for the cfg naming.

Jan-Mathijs Schoffelen - 2013-01-25 13:45:42 +0100

in ft_prepare_mesh the editing functionality is enabled when specifying cfg.interactive='yes'; I'd say it makes sense to also call it like this in ft_volumesegment

Robert Oostenveld - 2013-01-25 13:57:39 +0100

(In reply to comment #5) If we switch to FSL as yet another alternative method (or collection of methods) for segmentations, would the code not become more manageable with switch method case spm case fsl case manual ... otherwise error end % case than with if cfg.interactive==yes .. else switch method case spm case fsl case manual end % case end % if so rather to sticking to the old cfg.interactive and duplicating it, please also judge whether cfg.interactive should not disappear altogether in favor of method=manual. @Lilla, what do you think?

Jan-Mathijs Schoffelen - 2015-02-11 15:21:29 +0100

The function as such exists.