[FieldTrip] source statistics on atlas-based ROIs

[Joram van Driel]

Dear community,

I am doing a source analysis on Neuromag data; I used the DICS beamformer
to localize theta-band sources, and want to contrast two conditions of a
Stroop task.

I used subject-specific grids pre-warped to MNI space. Everything seems to
work fine and I'm at the group level to do statistics.

However, I have specific hypotheses about anatomical locations, so I'd like
to do stats only within frontal cortex.

I've searched around the tutorial web pages and the mailing list archive,
and there should be an option for this in ft_sourcestatistics, via
ft_read_atlas and ft_volumelookup. Currently, my code is:

aal =
ft_read_atlas('Z:\Toolboxes\fieldtrip_github\fieldtrip\template\atlas\aal\ROI_MNI_V4.nii');

% find frontal regions
front_idx = strmatch('Front', aal.tissuelabel);

cfg = [];
cfg.inputcoord = 'mni';
cfg.atlas = aal;
cfg.roi = aal.tissuelabel(front_idx);
mask = ft_volumelookup(cfg, ICavg_int);

ICavg_int.mask = mask;
cfg               = [];
cfg.method        = 'ortho';
cfg.funparameter  = 'pow';
cfg.maskparameter = 'mask';
cfg.funcolormap = 'jet';
ft_sourceplot(cfg,ICavg_int);

This gives me a source plot with only the frontal regions, the rest masked
out; so the atlas lookup seems to work. Then for source stats, in addition
to the design parameters (as in
http://www.fieldtriptoolbox.org/example/source_statistics), I add:

cfg.atlas = aal;
cfg.roi = aal.tissuelabel(front_idx);
cfg.inputcoord = 'mni';

Then I call:

stat = ft_sourcestatistics(cfg, grandavgIC{:}, grandavgCG{:});

However, the results are exactly the same with or without the atlas info
attached to the cfg; all voxels are analyzed, and the obtained cluster
results are the same. So it looks like ft_sourcestatistics doesn't do
anything with the atlas info. In the help of ft_sourcestatistics, it says:


% FIXME the following needs to be reimplemented
%
% You can restrict the statistical analysis to regions of interest (ROIs)
% or to the average value inside ROIs using the following options:
%   cfg.atlas        = filename of the atlas
%   cfg.roi          = string or cell of strings, region(s) of interest
from anatomical atlas
%   cfg.avgoverroi   = 'yes' or 'no' (default = 'no')
%   cfg.hemisphere   = 'left', 'right', 'both', 'combined', specifying this
is
%                      required when averaging over regions
%   cfg.inputcoord   = 'mni' or 'tal', the coordinate system in which your
source
%                      reconstruction is expressed

Does this mean this functionality doesn't work (yet)? Will it in the (near)
future, and is there a workaround? Of note, I just updated to the newest
fieldtrip version.

Thanks in advance for any thoughts or suggestions,

- Joram

-- 
Joram van Driel, PhD
Postdoc @ Vrije Universiteit Amsterdam
Cognitive Psychology
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151112/0261d71f/attachment-0001.html>