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Bug 2768 - Cannot combine opacity and atlas in ft_sourceplot
| Status | CLOSED WONTFIX |
| Reported | 2014-11-26 23:01:00 +0100 |
| Modified | 2019-08-10 12:41:23 +0200 |
| Product: | FieldTrip |
| Component: | core |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | All |
| Importance: | P5 normal |
| Assigned to: | |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Jens Klinzing - 2014-11-26 23:01:43 +0100
Created attachment 678 All mentioned plots. When combining opacity and atlas masking in a source plot (no matter if slice, surface, or ortho) a strange plotting error arises. The chosen functional areas show the actual data but with a faint color overlay. The outer edge of the plot (outside of the functional areas and even outside the brain) is drawn fully opaque (s. attachment). Using the atlas alone works. Example code: cfg = []; cfg.method = 'ortho'; cfg.funparameter = 'avg.pow'; cfg.funcolormap = 'jet'; cfg.maskparameter = cfg.funparameter; cfg.opacitymap = 'vdown'; % same with 'auto' cfg.funcolorlim = [-2.01 2.01]; cfg.atlas = fullfile(home, '_fieldtrip','template','atlas','aal','ROI_MNI_V4.nii'); cfg.roi = labels_cerebrum; data.coordsys = 'mni'; ft_sourceplot(cfg, data) The cell array 'labels_cerebrum' just contains all 90 labels outside of cerebellum. All figures in the attachment are done with this code with just the respective parts commented out. Another (maybe related) problem is seen already when only using opacity for data containing negative and positive values. A dark blue frame is drawn around the plot. I solved this problem in the past by taking the vdown opacity map and setting the very first value to zero. All the best and keep up the good work! Jens
Robert Oostenveld - 2014-11-27 09:29:08 +0100
Hi Jens, for reproducing it would be good to know which MATLAB version on which platform you are using. thanks for reporting Robert
Jens Klinzing - 2014-11-27 11:25:08 +0100
The problem occurred on Linux CentOS 6.3/Matlab 2013b and Windows 7/2013a. Sorry for not stating that in my original post!
Jens Klinzing - 2014-11-27 14:24:39 +0100
(Fieldtrip version from Tuesday, Nov 25)
Jens Klinzing - 2014-11-27 16:31:47 +0100
Same problem with Windows 7/2014b.
Jens Klinzing - 2015-02-19 11:59:34 +0100
Created attachment 702 Plot with blue frame Plotted data 'source_diff' from the extended beamformer tutorial after interpolation. If masking is used it shows a blue frame covering parts of the mri.
Jens Klinzing - 2015-02-19 12:00:34 +0100
The latter problem (dark blue frame around plot when plotting negative and positive values with masking) has already been reported in 2012 here: http://mailman.science.ru.nl/pipermail/fieldtrip/2012-July/005440.html This bug is still in place. It can be reproduced by taking the tutorial dataset (see attachment "Plot with blue frame"): ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/beamformer_extended/source_diff.mat ...and plotting it like this (mri_mni is the MNI template mri): cfg_int = []; cfg_int.downsample = 1; cfg_int.parameter = 'avg.pow'; source_diff_int = ft_sourceinterpolate(cfg_int, source_diff, mri_mni); cfg = []; cfg.method = 'slice'; cfg.funparameter = 'pow'; cfg.maskparameter = 'pow'; ft_sourceplot(cfg,source_diff_int)
Jan-Mathijs Schoffelen - 2017-01-17 15:26:03 +0100
It's unclear what the status of this one is, but given the fact that we're severely underpowered in terms of people contributing to fixing issues on bugzilla, Robert and JM have decided to close the low-priority bugs for now. This in order to keep the number of open bugs manageable. Feel free to reopen it, if you are willing to move this one forward towards a more proper resolution.
Robert Oostenveld - 2019-08-10 12:35:13 +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 https://github.com/fieldtrip/fieldtrip/issues.