[Mne_analysis] coordinate frame numbering

parham hashemzadeh ph442 at cam.ac.uk
Wed Apr 13 06:58:28 EDT 2016
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Dear all
  I would be very grateful, if you would kindly clarify the coordinate 
system numbering for me in MNE. I have the following questions:
Question:
1.  (i) Device coordinate coord_frame=1
     (ii) Head coordinate coord_frame =2?
    (iii)Surface RAS coord_frame=3
    (iv) RAS=4

2. In MNE-Python fwd['info']['chs'][0 ] "below "
  (a) Does the value coord_frame=1 mean it is the device coordinate?
   (b) Where is the coil transformation matrix stored(according to the 
transformation matrix diagrams for different coordinate systems) ?
   fwd['info']['chs'][0]
Out[36]:
{'cal': 3.1600000394149674e-09,
  'ch_name': u'MEG 0113',
  'coil_type': 3012,
  'coord_frame': 1,
  'kind': 1,
  'loc': array([-0.1066    ,  0.0464    , -0.0604    , -0.0127    ,  
0.0057    ,
         -0.99990302, -0.186801  , -0.98240298, -0.0033    , -0.98232698,
          0.18674099,  0.013541  ]),
  'logno': 113,
  'range': 0.00030517578125,
  'scanno': 1,
  'unit': 201,
  'unit_mul': 0}

3.  In MNE-Python the forward data structure fwd, it says that for the 
EEG sensor the coord_frame=4. Does it mean that the electrode position 
has undergone the transformations from Head->Surface RAS->RAS??
fwd['info']['chs'][350]
Out[39]:
{'cal': 0.0001976000057766214,
  'ch_name': u'EEG 045',
  'coil_type': 1,
  'coord_frame': 4,
  'kind': 2,
  'loc': array([-0.06437745, -0.04527977,  0.0883803 ,  0.00235201,  
0.11096951,
         -0.03500458,  0.        ,  1.        ,  0.        ,  0.        ,
          0.        ,  1.        ]),
  'logno': 45,
  'range': 0.00030517578125,
  'scanno': 360,
  'unit': 107,
  'unit_mul': 0}

4. Sorry for being paranoid!!! But, does the ""Matrix""" below
fwd['info']['mri_head_t']
Out[42]:
<Transform  |  MRI (surface RAS)->head>
[[ 0.99930958  0.00998476 -0.03578702 -0.00316745]
  [ 0.01275932  0.81240469  0.5829544   0.00685511]
  [ 0.03489422 -0.58300841  0.81171643  0.02888404]
  [ 0.          0.          0.          1.        ]]
mean that it is the inverse of T2, i.e T2inv???? I ask this because in 
order to go from Head->Surface RAS, you need the T2 matrix for 
transformation.
Many Many thanks
Sorry for asking what appears to be trivial questions??
Many thanks
best regards parham hashemzadeh





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