[FieldTrip] Atlas plot - region highlight

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

Hi Rita,

I am not sure what you’re after exactly, since your question is still a bit underspecified. Specifically, I am not clear on what you mean exactly with ‘my 3D head model plot’. 

The AAL is a ‘volumetric’ atlas, that indicates for all voxels in a standardised coordinate system the ‘area’ to which that voxels belongs. As far as I know, this atlas does not provide Brodmann areas, but rather provides more generic lobe and gyrus related anatomical labels.

Yet, if it is about visualization, as long as your atlas is in the same coordinate system (and voxel space) as a corresponding anatomical image, you could do something like this:

cd <directory-to-fieldtrip>/template/anatomy
x=ft_read_mri('single_subj_T1.nii');
cd <directory-to-fieldtrip>/template/atlas/aal
y=ft_read_atlas('ROI_MNI_V4.nii');

% you can only proceed with the following if x.transform and y.transform (as well as x.dim and y.dim) are identical, otherwise you need to interpolate the atlas onto the anatomy


y=ft_datatype_segmentation(y,’segmentationstyle’,’probabilistic’);
x.data = double(y.('name-of-the-area-you-want-to-show’));

cfg = [];
cfg.funparameter = ‘data’;
cfg.method = ’slice’;
ft_sourceplot(cfg, x);


It could also be, that you are seeking for something else, e.g. a way to evaluate the atlas label of the voxel that has a position that is closest to the estimated dipole position. This of course would require some different functionality.

Best wishes,

Jan-Mathijs



> On 10 Jan 2022, at 00:38, Rita Martins via fieldtrip <fieldtrip at science.ru.nl> wrote:
> 
> 
> Hello fieldtrip community,
> 
> For my master's dissertation project, I'm currently doing dipole fit analysis on a Neuromag system signal.
> 
> To confirm that the dipole locations are on Brodmann's motor cortex area, I would like to highlight this particular brain region in my 3D head model plot. I've tried to use AAL atlas, but I can't seem to get it working. I've followed several tutorials but I've had issues even with sample data from fieldtrip tutorials.
> 
> Is it possible to achieve this, that is, have this region highlighted, by using AAL atlas, from a fieldtrip template?
> 
> Best regards,
> Rita Martins 
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