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Bug 678 - volume conductor doesn't look good
| Status | CLOSED FIXED |
| Reported | 2011-05-19 20:22:00 +0200 |
| Modified | 2011-06-01 13:40:49 +0200 |
| Product: | FieldTrip |
| Component: | forward |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Linux |
| Importance: | P1 normal |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Lilla Magyari - 2011-05-19 20:22:35 +0200
Hi, I have discovered that the problem that is shown in the tutorial page: http://fieldtrip.fcdonders.nl/development/minimum_norm_estimate_in_fieldtrip at Figure 5. is probably due to the problem with the volume conductor. On the figure, the sourcespace looks to be larger than the volume conductor. I looked at the volume conductor that I used for creating the figure and I have discovered that there parts at the top of the head that are missing. You can check this with the roboos/data/lilmag/tutorial vol7 structure. Other version of the volume conductor (vol6) looks to be ok (no parts are missing). I made a test. When I used the following script to do the segmentation: cfg = []; cfg.coordsys = 'ctf'; cfg.smooth = 5; cfg.threshold = 0.5; seg7 = ft_volumesegment(cfg, mrirs5); cfg = []; vol7 = ft_prepare_singleshell(cfg, seg7); I got the bad volume conductor, but when I did the following: cfg = []; cfg.coordsys = 'ctf'; %cfg.smooth = 5; %cfg.threshold = 0.5; seg6 = ft_volumesegment(cfg, mrirs5); save seg6 seg6 cfg = []; vol6 = ft_prepare_singleshell(cfg, seg6); The vol6 was OK. The difference is that I haven't used the smooth and threshold parameters for the segmentation. The question is if there is way to do the segmentation that I get a brainmask but I also can create the volume conductor out of the same variable. You can find all these variables in the mentioned directory. thanks for help. Lilla
Jan-Mathijs Schoffelen - 2011-05-20 08:59:33 +0200
Hi Lilla, Good detective work. I think I will ensure/enforce sensible options in ft_volumesegment to prevent people from specifying nonsense cfg's ( ;o) ). It seems the function just needs to allow/disallow certain cfg-options. BW, JM
Lilla Magyari - 2011-05-25 11:46:58 +0200
(In reply to comment #1) > Hi Lilla, > > Good detective work. I think I will ensure/enforce sensible options in > ft_volumesegment to prevent people from specifying nonsense cfg's ( ;o) ). It > seems the function just needs to allow/disallow certain cfg-options. > > BW, > > JM hi JM, I have looked at the new form of the function and it looks good. But I still have to the question if I have to run two times ft_volumesegment if I want to have a skull stripped anatomy and also a structure that I can input to ft_prepare_singleshell? lilla
Jan-Mathijs Schoffelen - 2011-05-25 12:00:18 +0200
can't you do something like cfg.output = {'skullstrip' 'brain'} prior to calling ft_volumesegment? I thought this gives you the skullstripped anatomy, as well as the brain mask