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Bug 1355 - there is a bug in ft_volumesegment
| Status | CLOSED WORKSFORME |
| Reported | 2012-03-02 14:39:00 +0100 |
| Modified | 2019-08-10 11:55:40 +0200 |
| Product: | FieldTrip |
| Component: | preproc |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Windows |
| Importance: | P3 critical |
| Assigned to: | |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Ali Bahramisharif - 2012-03-02 14:39:32 +0100
if you run: mri = ft_read_mri('berends_s.mri'); ft_determine_coordsys(mri) it looks fine. However, if you after that run: cfg = []; cfg.coordsys = 'ctf'; segmentedmri = ft_volumesegment(cfg, mri); ft_determine_coordsys(segmentedmri) you get the following error : " The positive x-axis is pointing towards the right The positive y-axis is pointing towards anterior The positive z-axis is pointing towards superior ??? Error using ==> ft_determine_coordsys>xyz2label at 302 unknown coordsys Error in ==> ft_determine_coordsys at 163 [labelx, labely, labelz] = xyz2label(data.coordsys); " From the axes, it is obvious that there is a confusion between the coordinate systems of the original mri and the segmented mri.
Jan-Mathijs Schoffelen - 2012-03-02 14:41:46 +0100
problem: the transformation matrix in the segmented volume does not reflect the transformation matrix in the input.
Ali Bahramisharif - 2012-03-02 14:46:14 +0100
Here is the link to the mri file used: ftp://ftp.fcdonders.nl/pub/temporary/ftbug/
Jan-Mathijs Schoffelen - 2012-03-02 14:52:46 +0100
problem: the transformation matrix in the segmented volume does not reflect the transformation matrix in the input.
Robert Oostenveld - 2012-03-02 15:35:49 +0100
I have downloaded the mri, and executed the same steps. I don't get a problem, but a meaningful figure. See attached.
Robert Oostenveld - 2012-03-02 15:36:18 +0100
Created attachment 235 screen shot with (correct) output
Robert Oostenveld - 2012-03-02 15:37:42 +0100
(In reply to comment #5) note that the segmentedmri contains the following >> segmentedmri segmentedmri = dim: [256 256 256] transform: [4x4 double] coordsys: 'ctf' unit: 'mm' gray: [256x256x256 double] white: [256x256x256 double] csf: [256x256x256 double] cfg: [1x1 struct] If yours is different, then that suggests that you are using an older fieldtrip version.
Ali Bahramisharif - 2012-03-02 15:59:41 +0100
(In reply to comment #6) I use the fieldtrip on mentat, and I have the following: segmentedmri = dim: [256 256 256] transform: [4x4 double] coordsys: 'spm' unit: 'mm' gray: [256x256x256 double] white: [256x256x256 double] csf: [256x256x256 double] cfg: [1x1 struct] The difference is coordsys which is spm in mine and is ctf in yours, although I specified it to be ctf! BTW, this is what I get: segmentedmri.transform = 0.9992 0.0370 0.0133 -95.7202 0.0393 -0.9428 -0.3311 149.2684 0.0003 0.3313 -0.9435 46.9203 0 0 0 1.0000 whereas: mri.transform = 0.0392 -0.9244 -0.3794 186.2394 -0.9992 -0.0370 -0.0133 95.7202 -0.0018 0.3796 -0.9252 91.4222 0 0 0 1.0000
Robert Oostenveld - 2012-03-02 16:22:17 +0100
(In reply to comment #7) It might be that you are using an incorrect version of fieldtrip on mentat, or an incorrect version of spm, or a combination of both. can you upload the segmentedmri variable in a mat file? can you copy-and-paste the output of "path" in MATLAB?
Ali Bahramisharif - 2012-03-02 16:34:25 +0100
(In reply to comment #8) The segmentedmri is in /home/common/temporary/4robert/ This is my path: /home/common/matlab/spm8/external/fieldtrip/specest /home/common/matlab/spm8/external/fieldtrip/inverse /home/common/matlab/spm8/external/fieldtrip/forward /home/common/matlab/spm8/external/fieldtrip/preproc /home/common/matlab/spm8/external/fieldtrip/trialfun /home/common/matlab/spm8/external/fieldtrip/statfun /home/electromag/alibah/matlab /home/common/matlab/spm8 /home/common/matlab/spm8/EEGtemplates /home/common/matlab/spm8/apriori /home/common/matlab/spm8/canonical /home/common/matlab/spm8/config /home/common/matlab/spm8/exec /home/common/matlab/spm8/external /home/common/matlab/spm8/external/bemcp /home/common/matlab/spm8/external/ctf /home/common/matlab/spm8/external/eeprobe /home/common/matlab/spm8/external/fieldtrip /home/common/matlab/spm8/external/fieldtrip/connectivity /home/common/matlab/spm8/external/fieldtrip/fileio /home/common/matlab/spm8/external/fieldtrip/plotting 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/opt/matlab2009b/toolbox/nnet/nnobsolete /opt/matlab2009b/toolbox/nnet/nnresource /opt/matlab2009b/toolbox/nnet/nnutils /opt/matlab2009b/toolbox/optim/optim /opt/matlab2009b/toolbox/optim/optimdemos /opt/matlab2009b/toolbox/shared/optimlib /opt/matlab2009b/toolbox/pde /opt/matlab2009b/toolbox/signal/signal /opt/matlab2009b/toolbox/signal/sigtools /opt/matlab2009b/toolbox/signal/sptoolgui /opt/matlab2009b/toolbox/signal/sigdemos /opt/matlab2009b/toolbox/slcontrol/slcontrol /opt/matlab2009b/toolbox/slcontrol/slctrlguis /opt/matlab2009b/toolbox/slcontrol/slctrlutil /opt/matlab2009b/toolbox/slcontrol/slctrldemos /opt/matlab2009b/toolbox/splines /opt/matlab2009b/toolbox/stats /opt/matlab2009b/toolbox/symbolic /opt/matlab2009b/toolbox/wavelet/wavelet /opt/matlab2009b/toolbox/wavelet/wmultisig1d /opt/matlab2009b/toolbox/wavelet/wavedemo
Jan-Mathijs Schoffelen - 2012-03-02 16:38:53 +0100
please remove /home/common/matlab/spm8 and all its subdirectories from the path and try again. there is an external/fieldtrip directory which most likely causes the problem -> old version
Robert Oostenveld - 2012-03-02 16:52:49 +0100
See also http://fieldtrip.fcdonders.nl/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path
Ali Bahramisharif - 2012-03-02 17:03:36 +0100
(In reply to comment #11) Right. The problem is resolved. I shouldn't have had spm8 in my path.
Robert Oostenveld - 2019-08-10 11:51:42 +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 describing the issue on https://github.com/fieldtrip/fieldtrip/issues.