[FieldTrip] Fwd: Coordsys issue ft_sourceplot
Andreas Sauer
sauer.mpih at googlemail.com
Tue Jun 21 22:14:25 CEST 2016
Dear Marc,
thanks for your comment! It works fine.
Best,
Andreas
2016-06-21 10:32 GMT+02:00 Marc Recasens <recasensmarc at gmail.com>:
> Dear Andreas,
>
> I managed to get the AAL atlas labels on ortho-plots by adding the same
> "coordsys" subfield in both atlas and data files (plus cfg.atlas). I use
> coordsys = 'spm' even though everything is "mni", I reckon doesn't matter
> as long as both files share the same "coordsys". Maybe there's a more
> elegant way to do it but that worked fine for me.
>
> atlas = ft_read_atlas(paths_to_AAL_atlas);
> % read aal atlas
> atlas.coordsys = 'spm';
> interpolated_data.coordsys = 'spm';
> cfg_plot = [];
> cfg_plot.method = 'ortho';
> cfg_plot.funparameter = 'pow';
> cfg_plot.atlas = atlas;
> ft_sourceplot(cfg_plot,interpolated_data);
>
> Hope it helps
> Marc
>
>
> On Mon, Jun 20, 2016 at 8:22 PM, Andreas Sauer <sauer.mpih at googlemail.com>
> wrote:
>
>> Dear Jan-Mathijs,
>>
>> sorry that I bring up that post again, but I am still having problems
>> with the different coordinate systems in my data.
>>
>> After replacing the .pos field in the source files with the one from the
>> "standard_sourcemodel3d5mm" ft_sourceplot works fine, i.e. the functional
>> data is not rotated anymore. However, the option cfg.atlas doesn't work
>> since I always get the error message "mismatch between the coord sys in the
>> atlas and the coord sys in the data...".
>>
>> I checked the atlas, the functional data (stat) and the anatomy I use for
>> interpolation with ft_determine_coordsys. All three files have RAS
>> orientation. If I change the anatomical label of the axes of the functional
>> data, ft says "neuromag". Unfortunately, the function atlas_lookup works
>> only with "mni", "tal" or "spm". So I see where the error messages comes
>> from... The difference between MNI and neuromas is the unit (mm resp. m),
>> so I thought to use ft_convert_units, but that doesn't work for functional
>> data.
>>
>> Is there any way that I can change the functional data to "MNI" (I
>> thought I did this already)? Sorry if this is a straight forward thing, but
>> I don't see where I make the mistake...
>>
>> Thanks a lot and best wishes,
>>
>> Andreas
>>
>> 2016-06-15 15:06 GMT+02:00 Schoffelen, J.M. (Jan Mathijs) <
>> jan.schoffelen at donders.ru.nl>:
>>
>>> Are you sure that you use the pos-field from the template, i.e. from the
>>> standard_sourcemodel3d5mm?
>>>
>>> Best,
>>> Jan-Mathijs
>>>
>>> On 15 Jun 2016, at 14:31, Andreas Sauer <sauer.mpih at googlemail.com>
>>> wrote:
>>>
>>> Dear Jan,
>>>
>>> thank you for your email and the example code!
>>>
>>> I tried both ways to convert the coord systems, but unfortunately it
>>> still doesn't work.
>>>
>>> Since I used the tutorial procedure to create my sourcemodel (
>>> http://www.fieldtriptoolbox.org/tutorial/sourcemodel#subject-specific_grids_that_are_equivalent_across_subjects_in_normalized_space)
>>> I tried first with the easy way of only replacing the .pos field. But the
>>> plots don't change, the sources are still rotated by 90 degrees. Actually,
>>> the .pos fields are already the same before replacing it (see pic). Is
>>> there some error in my code?
>>>
>>>
>>> *% Step1: Load mri file*
>>> *mri =
>>> ft_read_mri('/data/home1/asauer/Projects/RPScZ/Analysis/Beamforming/MRI/HSM12_V2.mri');*
>>>
>>> *% Step 2: Segment the template brain and construct a volume conduction*
>>> *% model (i.e. head model): this is needed for the inside/outside
>>> detection of voxels*
>>> *cfg = [];*
>>> *cfg.output = 'brain';*
>>> *segmentedmri = ft_volumesegment(cfg,anatomy);*
>>>
>>> *cfg = [];*
>>> *cfg.method = 'singleshell';*
>>> *vol = ft_prepare_headmodel(cfg,segmentedmri);*
>>> *vol = ft_convert_units(vol,'m');*
>>> *figure; ft_plot_sens(sens,'style','*b'); hold on; ft_plot_vol(vol)*
>>>
>>> *% Step 3: Load sourcemodel *
>>>
>>> *load(fullfile(ft_path,'template/sourcemodel/standard_sourcemodel3d5mm'));*
>>> *template_grid = sourcemodel;*
>>> *clear sourcemodel*
>>>
>>> *% Step 4: Make sourcemodel*
>>> *cfg = [];*
>>> *cfg.grid.warpmni = 'yes';*
>>> *cfg.grid.template = template_grid;*
>>> *cfg.grid.nonlinear = 'yes';*
>>> *cfg.mri = mri;*
>>> *cfg.grid.unit = 'm';*
>>> *grid = ft_prepare_sourcemodel(cfg);*
>>> *figure; hold on;*
>>> *ft_plot_vol(vol,'facecolor','cortex','edgecolor','none'); alpha 0.5;
>>> camlight;*
>>> *ft_plot_mesh(grid.pos(grid.inside,:));*
>>>
>>>
>>> The only thing that is different from the tutorial is the unit
>>> conversion...
>>>
>>> After that I tried the transformation. All worked well until the source
>>> interpolation. ft_sourceinterpolation throws this error:
>>>
>>> *Attempted to access sel(1); index out of bounds because numel(sel)=0.*
>>>
>>> *Error in ft_sourceinterpolate>my_interpn (line 508)*
>>> * ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num);*
>>>
>>> *Error in ft_sourceinterpolate (line 393)*
>>> * interp.inside( sel) = my_interpn(double(functional.inside),
>>> ax(sel), ay(sel), az(sel), 'nearest', cfg.feedback);*
>>>
>>>
>>> which, to be honest, I don't really understand. Sorry...
>>>
>>> Best wishes,
>>>
>>> Andreas
>>>
>>>
>>> 2016-06-14 9:41 GMT+02:00 Schoffelen, J.M. (Jan Mathijs) <
>>> jan.schoffelen at donders.ru.nl>:
>>>
>>>> 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
>>>> Deutschordenstraße 46
>>>> 60528 Frankfurt am Main
>>>> Germany
>>>>
>>>> T: +49 69 96769 278
>>>> F: +49 69 96769 327
>>>> Email: sauer.mpih at gmail.com
>>>> www.brain.mpg.de
>>>> <Rotated_Source.png>_______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>>
>>> --
>>> Dipl.-Psych. Andreas Sauer
>>> Max Planck Institute for Brain Research
>>> Deutschordenstraße 46
>>> 60528 Frankfurt am Main
>>> Germany
>>>
>>> T: +49 69 96769 278
>>> F: +49 69 96769 327
>>> Email: sauer.mpih at gmail.com
>>> www.brain.mpg.de
>>> <pos_fields.png>_______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>> --
>> Dipl.-Psych. Andreas Sauer
>> Max Planck Institute for Brain Research
>> Deutschordenstraße 46
>> 60528 Frankfurt am Main
>> Germany
>>
>> T: +49 69 96769 278
>> F: +49 69 96769 327
>> Email: sauer.mpih at gmail.com
>> www.brain.mpg.de
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> Marc Recasens
>
> Tel.: +44 7845810006
> Tel.: +34 639241598
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
--
Dipl.-Psych. Andreas Sauer
Max Planck Institute for Brain Research
Deutschordenstraße 46
60528 Frankfurt am Main
Germany
T: +49 69 96769 278
F: +49 69 96769 327
Email: sauer.mpih at gmail.com
www.brain.mpg.de
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