[FieldTrip] anatomical labelling of dipole positions

[Tom Marshall]

Hi Eelke,

Fantastic! I'm now almost where I want to be...

Now I have the MNI co-ordinate, and plotting:

cfg=[];
cfg.location=mnipos;
cfg.locationcoordinates='head';
cfg.atlas='/home/common/matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii';
cfg.funparameter='anatomy';
ft_sourceplot(cfg,normalised);

Gives me the plot with the dipole position where I expect it (based on 
where it was pre-warping) and an anatomical label from the AAL atlas. So 
far so good.

I'd like to go one better though, and directly look up the label from 
the atlas. ft_volumelookup returns an anatomical label if you give it a 
binary mask, so I could try to create a volume-sized mask full of zeroes 
with a single 1 at 'mnipos'. However, mnipos is an MNI co-ordinate, and 
I would need to specify the 1 in voxel co-ordinates (ie, as an index in 
the matrix rather than a co-ordinate which could be -ve). How to convert 
the co-ordinate?

Best,
Tom

On 8/26/2014 6:03 PM, Eelke Spaak wrote:
> Hi Tom,
>
> ft_volumenormalise will allow you to normalise an anatomical volume to
> MNI space. The output of ft_volumenormalise will have a .params and
> .initial field. These you need, you can discard the actual normalised
> volumetric data. The fields contain the linear (.initial) and
> nonlinear (.params) warps needed to go from subject-specific to MNI
> space, and vice versa. Using these you can do something like:
>
> normalised = ft_volumenormalise([], mri);
> mnipos = ft_warp_apply(normalised.params,
> ft_warp_apply(normalised.initial, subjectpos), 'individual2sn');
>
> where subjectpos is an Nx3 array of subject-specific coordinates, and
> mnipos will of course be Nx3 in MNI space.
>
> In case of questions we can discuss tomorrow in person :)
>
> Best,
> Eelke
>
> On 26 August 2014 17:49, Tom Marshall <t.marshall at fcdonders.ru.nl> wrote:
>> Hi Trippers,
>>
>> I have performed dipole fitting on some data and I would like to identify
>> the anatomical regions in which various dipoles are located - ie, to make
>> statements of the sort, 'dipole X was (best) localised to the right superior
>> parietal cortex'. Specifically - I have the output from ft_dipolefitting
>> which gives positions in the head space of the individual subjects, and I
>> would like to anatomically label the dipoles according to the AAL atlas,
>> which is based on the MNI template brain.
>>
>> I *think* what I will need to do is apply some warping of the subject MRI to
>> the MNI template, and then apply the same warping to the dipole co-ordinate.
>> However it is not clear to me how to warp a single point, rather than an
>> entire volume. Is there some fieldtrip function that could be used for this?
>>
>> I do not think the approach detailed in
>> <http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space>
>> will be much use here, since (if I understand correctly) the MNI-aligned
>> grid created here would only be used as a starting point for
>> ft_dipolefitting. In the end a given dipole might not correspond to any grid
>> point.
>>
>> Can anybody advise me on how to set about this?
>>
>> Thanks a lot.
>>
>> Best,
>> Tom
>>
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