[FieldTrip] using the PALS B12 atlas with fieldtrip

Robert Oostenveld r.oostenveld at donders.ru.nl
Thu Dec 6 22:58:37 CET 2012

Hi Fred

That is an intersting and timely question, as it is something that we are presently working on for the Human Connectome Project. So for some parts FieldTrip might already help you out, for some other parts there still might be some work to do.

The idea is that you would start with FT_READ_ATLAS. That represents the output structure either in the format as described in FT_DATATYPE_PARCELLATION (if it is a surface description) or as FT_DATATYPE_SEGMENTATION (if it is a 3-D volumetric description). See the help of those functions.

Since the atlas is for a template MRI, and the MEG source reconstruction needs to be done in individual coordinates (with the individual head model), you have to derive the spatial mapping from individual T1 to template/atlas T1, and then apply the inverse mapping on the template mesh. The individualized mesh can then be used as source space (i.e. into cfg.grid for FT_SOURCEANALYSIS). Once you have the source reconstruction on all vertices of of the mesh, you can call FT_SOURCEPARCELLATE (which is not in the release version yet, but a skelleton exists, see also http://bugzilla.fcdonders.nl/show_bug.cgi?id=1775) which collapses the estimated source data over all vertices within each parcel to a single parcel-estimate.

We are considering other alternatives for the source reconstruction, but this is more or less the first approach that we want to enable. However, we are presently not working with an atlas sheet, but rather with individual parcellated cortical sheets obtained from Freesurfer. So the step with the warp from atlas/template space to individual head space is one that we don't have to do for the HCP.  

It would be nice if we could get an example script on the fieldtrip wiki that demonstrates this. I hope that these guidelines provide you with some starting points. If you see parts of functionality that are still missing in fieldtrip to get the full pipeline to work, please let us know (e.g. through bugzilla).


On 6 Dec 2012, at 10:05, Frederic Roux wrote:

> Dear all,
> I was wondering if anyone had some partical experience or
> an idea on how to use the PALS B12 atlas provided by the Surface
> Management System DataBase  (Sumsd), to generate a template brain in
> fieldtrip which can then be used for source reconstruction.
> So far I am doing my source reconstruction based on 
> individual MRs morphed onto the MNI template brain.
> But I'd be intersted in knowing if it would make a
> difference if I use a different template.
> I've seen publications were people have done this
> so I know that in principle it should be possible. I just haven't
> found a practical way to read in the  atlas data with fieldtrip yet.
> The data can be found here:
> http://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06
> If you have any thoughts or comments on this, I'd be
> happy if you could share them with me.
> Best,
> Fred
> Frédéric Roux
> Postdoctoral Researcher
> www.bcbl.eu
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> fieldtrip at donders.ru.nl
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