[FieldTrip] Coordsys issue ft_sourceplot

[Schoffelen, J.M. (Jan Mathijs)]

Dear Andreas,

after having calculated the sources of a MMN paradigm (4D-system), I’d like to plot the results on one of the anatomy template files in the fieldtrip directory (single_subj_T1_1mm.nii) or alternatively on a MNI T1 template file (mni_icbm152_t1_tal_nlin_sym_09a.nii). Unfortunately, this is not working well… As you can see on the attached picture, the functional data is rotated by 90 degrees.

I guess that something gets mixed because of the different coordsystems of functional and anatomical data. The functional data is 4D, which means ALS orientation. The anatomical is MNI, so RAS orientation. The plotting works fine, if I use a mri file which was converted in field trip (V2.mri) and therefore is also in ALS orientation. However, the anatomy doesn’t look very pretty…

Is there any way that I can transform the functional data to RAS orientation or the anatomical data to ALS orientation, respectively?

I tried with ft_volumerealign. However, since the template file has no fiducials, it is hard to really precisely do this.

Fair point. I would however do it the other way around, using the V2 to get the transformation from voxel space to MNI-RAS, and then use the inverse of the transformation on the functional data: in this case you could use ft_volumenormalise, with cfg.nonlinear = ‘no’. Alternatively, if you are using this procedure: http://www.fieldtriptoolbox.org/tutorial/sourcemodel#subject-specific_grids_that_are_equivalent_across_subjects_in_normalized_space, you could directly replace the source.pos of your functional data with the template.pos and then do the interpolation.

To summarize:

either:

mri = ft_read_mri(‘V2.mri’);
mri.coordsys = ‘bti’;

cfg = [];
cfg.nonlinear=’no’;
mrin = ft_volumenormalise(cfg, mri);

transform_vox2bti = mri.transform;
transform_vox2spm = mrin.transform;
transform_bti2spm = transform_vox2spm/transform_vox2bti
source = ft_transform_geometry(transform_bti2spm, source);

source_int = ft_sourceinterpolate(somecfg, source, niceanatomical);

or:

source.pos = templat.pos;
source_int = ft_sourceinterpolate(somecfg, source, niceanatomical);

Best,
JM



Any input on how to plot the sources on one of these nice anatomical files is highly appreciated!

Thanks and best regards,

Andreas


--
Dipl.-Psych. Andreas Sauer
Max Planck Institute for Brain Research
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Germany

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