[FieldTrip] MNE-sample data set on Fieldtrip.

parham hashemzadeh ph442 at cam.ac.uk
Wed Apr 27 12:49:18 CEST 2016

Dear All
  I was hoping to perform a complete source analysis using FieldTrip on 
the MNE-sample data set.
  The link to the MNE data set link is given below:
  I am terribly confused on how to align the MRI coordinates to MEG. The 
MEG system is a neuromag306. The function  
hdr=ft_read_header(raw_data_set_filename) reads fiducial marks
HPI. It is contained in hdr.orig.dig.
Also shape = ft_read_headshape(raw_data_set_filename) gives a structure
shape =

          pos: [143x3 double]
          fid: [1x1 struct]
        label: {143x1 cell}
     coordsys: 'neuromag'
         unit: 'cm'
          pnt: [143x3 double]

where the shape.fid has the nasion, lpa and rpa. I have the following 
1. It appears to me that the MRI coordinate system is already spm.
   Axis X :Left to right.
   Axis Y: Posterior to Anterior.
   Axis Z: bottom to top.

2. How can I realign the MRI to MEG?
               a) Interactively: ft_volumerealign
               b) Should I use the information in shape to have it done 
I think, it would be unwise to define my own lpa, rpa and nasion.
3. What is the relationship between HPI coil coordinates and the lpa, 
rpa and nasion coordinates? Are there scripts that relate the two.
4. Has anyone ever created a script to use Fieldtrip to analyze this 
specific data set?

5. The MEG sensors are in a different coordinate frame "1" as opposed to 
head coordinates (Electrodes). Do I have to make sure that these 
coordinates are transformed to head coordinates prior to 
ft_prepare_leadfield calculations? or is this done automatically by 

I just have the feeling that it would be unwise to do this interactively 
because of the existence of the fiducial markers.

Many thanks if you are able to help me.

best regards
Parham Hashemzadeh
Research Associate
Department of Applied Mathematics and Theoretical Physics
University of Cambridge, UK.
email: hashemzadeh at damtp.cam.ac.uk

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