[Mne_analysis] coordinate frame numbering
parham hashemzadeh
ph442 at cam.ac.uk
Wed Apr 13 06:58:28 EDT 2016
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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