[FieldTrip] Using an fMRI cluster as an ROI

Pelt, S. van (Stan) stan.vanpelt at donders.ru.nl
Tue Jul 26 09:12:59 CEST 2016

Hi Ross,

I think what you looking for is explainef in this turorial:

Make sure that you first warp the subject's brain coordinates to MNI coordinates. Then enter your ROI coordinates at cfg.grid.pos and run the lcmv beamformer to get the spatial filter that is specific of your ROI peak MNI coordinates.

Hope that helps.


Op 25 jul. 2016 om 14:06 heeft Julian Keil <julian.keil at gmail.com<mailto:julian.keil at gmail.com>> het volgende geschreven:

Hi Ross,

one way to attempt this, is to create a 3D grid on your fMRI data, so that each voxel is a grid point.
Then you can compute the distance between grid points from the fMRI grid and your virtual electrode grid and find the nearest neighbours.
This sould work for the whole brain as well as for predefined ROIs.

I've attached a function I use for similar problems. I'm sure there are more elegant ways but this works for me. It won't do exactly what you want to do, but maybe some bits and pieces can help you along.

Good luck,


Am 25.07.2016 um 13:47 schrieb Ross Wilson:

Hello all!

I am attempting to use an fMRI cluster as an ROI to look at virtual electrode timecourses post-beamforming.

I have been using the aal atlas to find virtual electrodes of maximum change between baseline and stimulus period within, for example, the motor cortex afer beamforming. However, the virtual electrodes found are not necessarily in a position similar to that of the fMRI cluster and I’d like to be more specific than that if possible.

The template grid I have been using for beamforming is created from the T1 (code as below, in MNI space: …fieldtrip\external/spm8/templates/T1.nii). Is it possible to transform an fMRI cluster (in MNI space) onto the template grid so that the data from specific grid points relating to that cluster can be extracted post-beamforming??

Any help with this would be great!

Thank you,

%%%tempale grid creation
T1 = ft_read_mri('F:\fieldtrip\external/spm8/templates/T1.nii');
T1.coordsys = 'spm';

cfg          = [];
template_seg = ft_volumesegment(cfg, T1);

cfg          = [];
cfg.method   = 'singleshell';
template_vol = ft_prepare_headmodel(cfg, template_seg);
template_vol = ft_convert_units(template_vol, 'cm');

cfg = [];
cfg.grid.xgrid  = -20:0.5:20;
cfg.grid.ygrid  = -20:0.5:20;
cfg.grid.zgrid  = -20:0.5:20;
cfg.grid.unit   = 'cm';
cfg.grid.tight  = 'yes';
cfg.inwardshift = 0.15;
cfg.vol        = template_vol;
template_grid  = ft_prepare_sourcemodel(cfg);
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