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Bug 621 - creating a brainmask in MNE pipeline is not in FT style
| Status | CLOSED FIXED |
| Reported | 2011-04-28 13:59:00 +0200 |
| Modified | 2011-05-25 15:05:48 +0200 |
| Product: | FieldTrip |
| Component: | forward |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Windows |
| Importance: | P1 enhancement |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Lilla Magyari - 2011-04-28 13:59:00 +0200
Hi, I am creating a brainmask after segmenting the mri, the following way in the MNE pipeline: % load seg; % this was created in the 3. step (segment) mask = seg.gray + seg.white + seg.csf; spm_smooth(mask,mask,5); mask = imfill(mask>0.2, 'holes'); brainmask = double(mri_tal.anatomy).*double(mask); save brainmask brainmask; This piece of code doesn't follow the regular FieldTrip style. I am wondering if the following code would do the same (recently written by Cristiano): cfg=[]; cfg.smooth = 5; cfg.threshold = 0.5; segment = ft_volumesegment(cfg, mri); it is supposed to output not only the gray/white/csf segment, but also segment.brainmask. Would be this the same as the brainmask above? (For example, the threshold seems to be different.) thanks for help Lilla
Jan-Mathijs Schoffelen - 2011-04-28 14:14:11 +0200
Yes, the functionality implemented in ft_volumesegment should give the brainmask, in much the same way as the outside fieldtrip computations. (this was actually implemented by me ;o) )
Lilla Magyari - 2011-05-09 10:31:21 +0200
(In reply to comment #1) > Yes, the functionality implemented in ft_volumesegment should give the > brainmask, in much the same way as the outside fieldtrip computations. (this > was actually implemented by me ;o) ) Hi Jan-Mathijs, and should I change the threshold to 0.2 in order to create the same brainmask (as it is now in the MNE pipeline) or should I leave it on 0.5? (in case the "threshold" of the ft_volumesegment refers to the imfill parameter) thanks for the help. Lilla
Lilla Magyari - 2011-05-09 11:22:49 +0200
(In reply to comment #2) > (In reply to comment #1) > > Yes, the functionality implemented in ft_volumesegment should give the > > brainmask, in much the same way as the outside fieldtrip computations. (this > > was actually implemented by me ;o) ) > Hi Jan-Mathijs, > and should I change the threshold to 0.2 in order to create the same brainmask > (as it is now in the MNE pipeline) or should I leave it on 0.5? (in case the > "threshold" of the ft_volumesegment refers to the imfill parameter) > thanks for the help. > Lilla P.S.: Meanwhile I have checked the script, the ft_volumesegment does not seem to use imfil, so those numbers refer to different things. I will just use ft_volumesegment for creating brainmask as it is in the help of the function. Sorry for the unnecessary question, Lilla