[FieldTrip] cluster-based permutation tests on MNE-surface data

Meeren.H.K.M. hanneke.meeren at uvt.nl
Thu Dec 30 00:18:04 CET 2010

Dear Jan-Mathijs, 

Thank you for your quick answer. I have used the MNE/mne_analyze stream developed by Matti Hamalainen which implements the anatomically-constrained noise-normalized MNE 
(Dale et al.2000). The spatial structure of the data is indeed the cortical sheet segmented and reconstructed using Freesurfer. The individual cortical sheets were morphed onto each other using Matti's mne-stream which performs intersubject alignment of cortical landmarks based on a spherical surface-based coordinate system according to the method of  Fischl et al. (1999, Hum. Brain Mapping 8:272–284). I it makes use of a Freesurfer algorithm.   

Although the cortical sheet can functionally be considered as a folded 2D-sheet, computation-wise it is a 3D-patch of vertices, with each vertex having an x, y and z-coordinate, being the positions of the dipoles. I presume FT_SOURCESTATISTICS uses a 3D-voxel-grid, with the neighbors of each voxel being automatically defined on the basis of this grid (?). The trick would be then to translate the 3D-patch into a 3D-grid..., or not? No, I haven't thought of it yet how to do this. Also I don't know in which field and which format I should put the spatial info..

Alternatively, I was wondering whether I could work my way around it by using FT_TIMELOCKSTATISTICS instead and to consider the vertices as a set of (intracranial) electrodes with their x,y,z coordinates (and their time-course!). For the spatial clustering I would need to generate a neighborhood-structure. I don't know, however, how I should exactly pass the vertex positions info to the function. Using cfg.elec or cfg.elecfile, or data.elec, but it is not clear to me what should be the exact format of the structure. It is also not clear to me whether it is necessary to give each vertex a label (in which field should I put this?), or whether only setting cfg.neigbourdist would do the trick. 

It would be very helpful to have an example EEG input dataset for FT_TIMELOCKSTATISTICS and an example input dataset for FT_SOURCESTATISTICS to see what the exact format of the data should be! I couldn't find either of them in the tutorial.   

Best regards, 


-----Original Message-----
From: jan-mathijs schoffelen <jm.schoffelen at gmail.com>
To: hanneke.meeren at uvt.nl
Date: Wed, 29 Dec 2010 16:43:42 +0100
Subject: Re: [FieldTrip] cluster-based permutation tests on MNE-surface data

Hi Hanneke,

Performing cluster based statistics on source reconstructed data based  
on a cortical sheet is as of yet not supported (I assume at least that  
you do the standard MNE cortical sheet reconstruction). At the moment,  
we are actually working on implementing an MNE-like pipeline in  
FieldTrip.Our first strategy would be to interpolate the 2D sheets  
onto a 3D volume, and use the standard machinery for statistics. Yet,  
another viable approach indeed would be to build in support for 2D- 
neighbourhood structures. Do you have any clear ideas on that? I would  
also be interested to see your recipe to warp the individual cortical  
sheets to a template.

Regarding the mailing list: the list is hosted on a new server since  
the beginning of December. Apparently the archives have not been moved  
along, or at least are not accessible. We'll look into this.

Best wishes,


PS: could you forward this message to the list; I am at home and  
cannot send mails from my regular account.

On Dec 29, 2010, at 4:25 PM, Meeren.H.K.M. wrote:

> Hi,
> I would like to perform cluster-based permutation tests on MNE- 
> surface data, which I obtained using the MNE/Freesurfer pipeline. So  
> rather than use the whole FT pipeline and start from scratch, I  
> would like to import my existing source data into FieldTrip, and  
> export the resulting stats to my own matlab visualization tools.  
> Reading the tutorial and reference documentation I understand that I  
> could directly call ft_sourcestatistics, but it is not clear to me  
> what the exact data structure should be for the source data and  
> which fields the cfg should contain. I could not find a tutorial- or  
> example dataset for ft_sourcestatistics.
> For each condition I have the source data in a (subjects x vertices  
> x time) 3d-array for each condition. Is it possible to have a time- 
> dimension in the source-data, or should I first convert to a two- 
> dimensional array subjects x vertices? In addition I have generated  
> a location matrix which contains the x, y, z - coordinates of the  
> vertices of my surface, which I presume is necessary to define  
> neighbors. It is however not clear to me how to pass the location  
> matrix to the function (should it be defined in a cfg field?). I  
> have also tried to search the archives of the discussion list but  
> was unable to find any messages before December 2010.
> Does anyone have an example dataset available that can be used as  
> input dataset for sourcestatistics, so I can see what the structure  
> of the data should be? Could someone clarify how I should define the  
> location data? Could someone help me out on how to search through  
> the old messages in the discussion list archives.
> Any help is greatly appreciated,
> Thanks a lot in advance,
> Hanneke
> ----------------------------------
> Hanneke K.M. Meeren, PhD.
> Research Fellow and Instructor
> Medical Psychology and Cognitive Neuroscience
> Tilburg University
> P.O. Box 90153
> 5000 LE Tilburg
> The Netherlands
> email: hanneke.meeren at uvt.nl
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Hanneke K.M. Meeren, PhD.
Research Fellow and Instructor
Medical Psychology and Cognitive Neuroscience
Tilburg University
P.O. Box 90153
5000 LE Tilburg
The Netherlands
email: hanneke.meeren at uvt.nl

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