[FieldTrip] reverse source interpolate?

[Erick Ortiz]

Dear Vitória and Cornelius,

this is a common problem, and maybe it would be good to clarify the
strategies that can be used here. I hope this can help others in a similar
situation, which I have found many times.

1) You are trying to convert voxel indexes to head (CTF) coordinates. In
this case, there are two mistakes in the code:
1a) pos = warp_apply( pinv( sourceNAIInt.transform ), posInt, 'homogeneous'
);
... should be done with sourceNAIInt, not mri. The transforms are
different, in general; e.g. note the downsample=2.
1b) use cfg.locationcoordinates = 'head', as commented by JM in a previous
post. Or remove this line, since 'head' is the default.

2) But if you are working with the same subject/grid, there is no need for
interpolation at all. Simply find the grid position with highest 'pow' and
take its position.
    [dummy,ind] = max(source.avg.pow);
    pos = source.pos(ind,:);

3) However, this is not possible when using different grids, e.g. in a
grand average in MNI coordinates. Find the peak ('pos') in the interpolated
volume, as in Cornelius' code, then find the index of the nearest grid
position for a common (again, MNI) grid. This is also in JM's message.

dpos = source.pos - repmat( pos, size(source.pos,1), 1 );
[dummy,ind] = min(sum(dpos.^2,2));

4) What I have been using, and strongly recommend, is an MNI grid warped to
the subject's anatomy, according to this procedure:
http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space

This would give you both the benefits of working in MNI coordinates, and
the ease of having a common grid across subjects (for instance, enabling
solution #2). Still, some projects do call for one of the other options.

Just a couple of details:
- Pay utmost attention to coordinate systems and units. For instance, it is
common to confuse unlabeled cm for mm, and either of these with voxels. Try
to also label all structures as CTF or SPM (MNI).
- Using pinv instead of inv is usually a good idea. Here, it is a not an
issue, but matrix inversion in MATLAB can lead to a world of hurt to the
unwary.

Best,
Erick



On Tue, Mar 11, 2014 at 4:04 PM, Vitoria Piai <v.piai.research at gmail.com>wrote:

>  Dear FT-ers,
>
> I found an old posting to the mailing list (see below) that never got
> answered so my question still holds: given a location I found in the
> interpolated source, how do I find back the same location in .pos of the
> non-interpolated data?
> I can try and go around it by finding the corresponding MNI coordinates in
> the interpolated data (which by now I have to do by hand, so not optimal
> anyways), and then look for those coordinates in .pos. But I was wondering,
> like Cornelius was in his post, whether there is a neater way to get this
> information.
>
> Thanks a lot for the help,
> Vitória
>
>
>    >>>>>>>>>>>>>>
>>
>> Hi mailing list,
>>
>> I'm still struggling with the conversion of coordinates between source and
>> interpolated source space.
>> For example, if i have the position of a single grid point how do i get
>> the
>> corresponding voxel  in the interpolated source structure. Or the other
>> way
>> around, how to get the grid point which corresponds to a voxel (e.g the
>> max
>> voxel) in the interpolated source structure.
>>
>> I think this should be a common problem when working with virtual
>> electrodes, shouldn't it?
>>
>> To make things easier i put together a example with the data from the
>> source tutorial where i tried to calculated the grid pos of the max voxel
>> in the interpolated source.
>>
>> clear all;
>> load sourcePost_nocon;               % source structure from tutorial
>> mri = ft_read_mri('Subject01.mri');  % mri of subject01 from tutorial
>>
>> sourceNAI = sourcePost_nocon;
>> sourceNAI.avg.pow = sourcePost_nocon.avg.pow ./
>> sourcePost_nocon.avg.noise;
>> sourceNAI=rmfield(sourceNAI,'freq'); % had to remove that to let
>>
>> cfg = [];
>> cfg.downsample = 2;
>> cfg.parameter = 'avg.pow';
>> sourceNAIInt = ft_sourceinterpolate(cfg, sourceNAI , mri);
>>
>> % Find position of max activity
>> [dum, maxindx] = max(sourceNAIInt.avg.pow(:));
>> [xi, yi, zi] = ind2sub(sourceNAIInt.dim, maxindx);
>> posInt=[xi, yi, zi];
>>
>> % Plot interpolated source with position of max activity
>> cfg              = [];
>> cfg.method       = 'ortho';
>> cfg.funparameter = 'avg.pow';
>> cfg.locationcoordinates = 'voxel';
>> cfg.location      = posInt;          % location of max activity is marked
>> correctly.
>> figure;
>> ft_sourceplot(cfg,sourceNAIInt);
>>
>> % Transform coordinate back to uninterpolated source???
>> dpos = warp_apply(inv(mri.transform), posInt, 'homogeneous');
>>
>>
>> % Plot uninterpolated source with position aquired from interpolated
>> source
>> cfg              = [];
>> cfg.method       = 'ortho';
>> cfg.funparameter = 'avg.pow';
>> cfg.locationcoordinates = 'voxel';
>> cfg.location      = dpos;               % unfortunately this coordinate is
>> obviously wrong!!! WHY?
>> figure;
>> ft_sourceplot(cfg,sourceNAI);
>>
>>
>> Unfortunately the solution of Jan Mathijs did not work, nor did mine :(
>>
>> Any ideas???
>>
>> Cornelius
>>
>>
>>
>
>
>
> _______________________________________________
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> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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