LORETA to Fieldtrip
litvak at TECHUNIX.TECHNION.AC.IL
Mon Mar 27 15:15:30 CEST 2006
I tried reading the SPM MRI file (single_subj_T1.mnc - is this the one you
meant?) but in the grid variables there are just indices in the matrix. So
how do I know the correspondence to LORETA voxels? Is there a way to put the
MNI grid there?
From: Robert Oostenveld [mailto:r.oostenveld at fcdonders.ru.nl]
Sent: Monday, March 27, 2006 2:43 PM
To: Vladimir Litvak
Subject: Re: Clusterrandanalysis
> The question is - can we build a gateway for reading LORETA files
> in FT and
> applying the same statistics as you use for the beamformer?
> shouldn't be something very complicated I think. The only problem
> is that
> LORETA uses a grid of 2394 voxels which are only in the gray matter
> there are some holes there) and it would probably be necessary to
> do some
> smoothing. Also one must write a routine for transforming from
> LORETA grid
> to your grid (based on Tailarach coordinates of the voxels).
I once started with implementing LORETA myself in sourceanalysis, but
never finished it. I don't consider LORETA to be too interesting for
MEG, although I do appreciate it's usefullness for EEG. I have been
in contact a couple of times with Roberto Pasqual-Marqui, and he told
me some of the details.
LORETA is using plain SPM/MNI coordinates, which can also be used in
FT. The holes can be dealt with in FT by specifying NaNs as
source.avg.pow,  as source.avg.mom, and by specifying the right
source.inside and source.outside vector (those are indices specifying
which voxels are inside the brain, or inside the gray matter if you
Writing a LORETA importer should be trivial, but I am not going to do
it myself. Please point the grad student to
and tell him to use volume.inside and volume.outside to "fill" the
non-gray matter so that the data fits into a 3D box.
volume = read_fcdc_mri(filename)
with filename being the canonical MRI from SPM (the collin27 one).
That should belp in getting it alligned with the proper
Once you can read a single LORETA volume into FT, then you can repeat
it for all subjects and do your statistics. Please address further
questions regarding this topic to the mailing list.
PS I don't think that you want to smooth, our source clustering is
aware of the grey/white matter differences (given the correct inside/
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