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Bug 523 - strange problems in a sourceanalysis pipeline
| Status | CLOSED WONTFIX |
| Reported | 2011-03-07 09:56:00 +0100 |
| Modified | 2011-03-16 17:11:58 +0100 |
| Product: | FieldTrip |
| Component: | core |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Mac OS |
| Importance: | P1 normal |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Jan-Mathijs Schoffelen - 2011-03-07 09:56:11 +0100
Dear Jen, Please create an attachment to this bug, which contains the non-interpolated source level data, so that I can have a look myself.
J - 2011-03-07 20:24:43 +0100
Created attachment 27 sourcetemp.avg.pow (input to ft_sourceinterpolate) saved as a text file Error message at matlab prompt when calling ft_volumenormalise: -------------------------------- the input is volume data with dimensions [256 256 256] not downsampling anatomy not downsampling avg.pow not downsampling inside converting input coordinates from CTF into approximate SPM coordinates ??? NaN's cannot be converted to logicals. Error in ==> spm_create_vol>create_vol at 102 if swapped, Error in ==> spm_create_vol at 14 v = create_vol(V(i)); Error in ==> volumewrite_spm at 67 Va = spm_create_vol(Va); Error in ==> ft_write_volume at 61 V = volumewrite_spm(filename, dat, transform, spmversion); Error in ==> ft_volumenormalise at 219 ft_write_volume([cfg.intermediatename,'_' tmp '.img'], data, 'transform', interp.transform, 'spmversion', cfg.spmversion); Error in ==> beamform_tse_commonfilter_v21spm2T1 at 181 sourcetempIntN = ft_volumenormalise(cfg, sourcetempInt);
Jan-Mathijs Schoffelen - 2011-03-08 08:31:10 +0100
Created attachment 28 test script used to reproduce the problem, and to compare spm2 vs spm8
Jan-Mathijs Schoffelen - 2011-03-08 08:32:07 +0100
Created attachment 29 volumewrite_spm fixed version, should be able to write volumes which come as boolean (writes them as double though)
J - 2011-03-08 21:18:23 +0100
Created attachment 30 error message when using attachment #29
J - 2011-03-08 21:19:09 +0100
the input is volume data with dimensions [256 256 256] not downsampling anatomy not downsampling avg.pow not downsampling inside converting input coordinates from CTF into approximate SPM coordinates performing the normalisation warping the invdividual anatomy to the template anatomy, using only linear transformations Smoothing by 0 & 8mm.. Coarse Affine Registration.. Fine Affine Registration.. creating normalised analyze-file for anatomy creating normalised analyze-file for inside creating normalised analyze-file for avg.pow the input is volume data with dimensions [181 217 181] ??? Undefined function or method 'parameterselection' for input arguments of type 'struct'. Error in ==> ft_volumewrite at 119 cfg.parameter = parameterselection(cfg.parameter, volume); Error in ==> beamform_tse_commonfilter_v21spm2T1 at 191 ft_volumewrite(cfg,sourcetempIntN); >> cfg=[]; %cfg.parameter='pow'; cfg.filename=filename; cfg.filetype='spm'; cfg.coordinates='spm'; cft.datatype='double'; ft_volumewrite(cfg,sourcetempIntN); ??? Error using ==> ft_checkconfig at 157 The field cfg.parameter is required Error in ==> ft_volumewrite at 78 cfg = ft_checkconfig(cfg, 'required', {'filename', 'parameter'}); >> cfg=[]; cfg.parameter='avg_pow'; cfg.filename=filename; cfg.filetype='spm'; cfg.coordinates='spm'; cft.datatype='double'; ft_volumewrite(cfg,sourcetempIntN); the input is volume data with dimensions [181 217 181] ??? Undefined function or method 'parameterselection' for input arguments of type 'struct'. Error in ==> ft_volumewrite at 119 cfg.parameter = parameterselection(cfg.parameter, volume);