[med-svn] [python-mne] 245/376: fixing manual
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:23:00 UTC 2015
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yoh pushed a commit to annotated tag v0.1
in repository python-mne.
commit aa4bf205f6fea4bf645625c04ebf701acb30a395
Author: Emily Ruzich <emilyr at nmr.mgh.harvard.edu>
Date: Thu May 12 16:43:41 2011 -0400
fixing manual
---
doc/source/manual/forward.rst | 52 ++++++++++---------------------------------
1 file changed, 12 insertions(+), 40 deletions(-)
diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst
index bc11b05..09cc8be 100755
--- a/doc/source/manual/forward.rst
+++ b/doc/source/manual/forward.rst
@@ -792,36 +792,8 @@ The columns of the tables contain the following data:
.. note:: The coil geometry information is stored in the file $MNE_ROOT/share/mne/coil_def.dat, which is automatically created by the utility mne_list_coil_def , see :ref:`BJEHHJIJ`.
-.. tabularcolumns:: |p{0.1\linewidth}|p{0.3\linewidth}|p{0.1\linewidth}|p{0.3\linewidth}|p{0.2\linewidth}|
-.. _BGBBHGEC:
.. table:: Normal coil descriptions. Note: If a plus-minus sign occurs in several coordinates, all possible combinations have to be included.
- ======= ================================================================ ==== =============================================================== ===============================================================
- Id Description n r/mm w
- ======= ================================================================ ==== =============================================================== ===============================================================
- 2 Neuromag-122 planar gradiometer 2 :math:`\pm (8.1, 0, 0)`mm INLINE_EQUATION
- 2000 A point magnetometer 1 :math:`(0, 0, 0)`mm INLINE_EQUATION
- 3012 Vectorview type 1 planar gradiometer 2 :math:`(\pm 8.4, 0, 0.3)`mm INLINE_EQUATION
- 3013 Vectorview type 2 planar gradiometer 2 :math:`(\pm 8.4, 0, 0.3)`mm INLINE_EQUATION
- 3022 Vectorview type 1 magnetometer 4 :math:`(\pm 6.45, \pm 6.45, 0.3)`mm INLINE_EQUATION
- 3023 Vectorview type 2 magnetometer 4 :math:`(\pm 6.45, \pm 6.45, 0.3)`mm INLINE_EQUATION
- 3024 Vectorview type 3 magnetometer 4 :math:`(\pm 5.25, \pm 5.25, 0.3)`mm INLINE_EQUATION
- 2000 An ideal point magnetometer 1 :math:`(0,0,0)`mm
- 4001 Magnes WH magnetometer 4 :math:`(\pm 5.75, \pm 5.75, 0)`mm INLINE_EQUATION
- 4002 Magnes WH 3600 axial gradiometer 8 :math:`(\pm 4.5, \pm 4.5, 0)`mm :math:`(\pm 4.5, \pm 4.5, 50)`mm INLINE_EQUATION
- 4003 Magnes reference magnetometer 4 :math:`(\pm 7.5, \pm 7.5, 0)`mm INLINE_EQUATION
- 4004 Magnes reference gradiometer measuring diagonal gradients 8 INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION
- 4005 Magnes reference gradiometer measuring off-diagonal gradients 8 INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION
- 5001 CTF 275 axial gradiometer 8 INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION
- 5002 CTF reference magnetometer 4 INLINE_EQUATION INLINE_EQUATION
- 5003 CTF reference gradiometer measuring diagonal gradients 8 INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION
- 5004 CTF reference gradiometer measuring off-diagonal gradients 8 INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION
- 6001 MIT KIT system axial gradiometer 8 INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION
- ======= ================================================================ ==== =============================================================== ===============================================================
-
-
-.. XXX : incomplete
-
.. tabularcolumns:: |p{0.1\linewidth}|p{0.3\linewidth}|p{0.1\linewidth}|p{0.25\linewidth}|p{0.2\linewidth}|
.. _CHDBDFJE:
.. table:: Accurate coil descriptions
@@ -1180,7 +1152,7 @@ The EEG sphere model definition file
For the computation of the electric potential distribution
on the surface of the head (EEG) it is necessary to define the conductivities
-(INLINE_EQUATION) and radiuses of the spherically
+(:math:`\sigma`) and radiuses of the spherically
symmetric layers. Different sphere models can be specified with
the ``--eegmodels`` option.
@@ -1202,7 +1174,7 @@ always provided. This model has the structure given in :ref:`BABEBGDA`
.. table:: Structure of the default EEG model
======== ======================= =======================
- Layer Relative outer radius INLINE_EQUATION (S/m)
+ Layer Relative outer radius :math:`\sigma` (S/m)
======== ======================= =======================
Head 1.0 0.33
Skull 0.97 0.04
@@ -1222,8 +1194,8 @@ and amplitudes are determined by minimizing the cost function:
.. math:: S(r_1,\dotsc,r_m\ ,\ \mu_1,\dotsc,\mu_m) = \int_{scalp} {(V_{true} - V_{approx})}\,dS
-where INLINE_EQUATION and INLINE_EQUATION are
-the locations and amplitudes of the approximating dipoles and INLINE_EQUATION and INLINE_EQUATION are
+where :math:`r_1,\dotsc,r_m` and :math:`\mu_1,\dotsc,\mu_m` are
+the locations and amplitudes of the approximating dipoles and :math:`V_{true}` and :math:`V_{approx}` are
the potential distributions given by the true and approximative
formulas, respectively. It can be shown that this integral can be
expressed in closed form using an expansion of the potentials in
@@ -1242,14 +1214,14 @@ location coordinates to the output file. Let
.. math:: G_k = [g_{xk} g_{yk} g_{zk}]
-be the INLINE_EQUATION matrix containing
-the signals produced by three orthogonal dipoles at location INLINE_EQUATION making
-up INLINE_EQUATIONthe gain matrix
+be the :math:`N_{chan} \times 3` matrix containing
+the signals produced by three orthogonal dipoles at location :math:`r_k` making
+up :math:`N_{chan} \times 3N_{source}` the gain matrix
.. math:: G = [G_1 \dotso G_{N_{source}}]\ .
With the ``--grad`` option, the output from mne_forward_solution also
-contains the INLINE_EQUATION derivative matrix
+contains the :math:`N_{chan} \times 9N_{source}` derivative matrix
.. math:: D = [D_1 \dotso D_{N_{source}}]\ ,
@@ -1257,11 +1229,11 @@ where
.. math:: D_k = [\frac{\delta g_{xk}}{\delta x_k} \frac{\delta g_{xk}}{\delta y_k} \frac{\delta g_{xk}}{\delta z_k} \frac{\delta g_{yk}}{\delta x_k} \frac{\delta g_{yk}}{\delta y_k} \frac{\delta g_{yk}}{\delta z_k} \frac{\delta g_{zk}}{\delta x_k} \frac{\delta g_{zk}}{\delta y_k} \frac{\delta g_{zk}}{\delta z_k}]\ ,
-where INLINE_EQUATION are the location
-coordinates of the INLINE_EQUATION dipole. If
+where :math:`x_k`, :math:`y_k`, and :math:`z_k` are the location
+coordinates of the :math:`k^{th}` dipole. If
the dipole orientations are to the cortical normal with the ``--fixed``
-option, the dimensions of INLINE_EQUATION and INLINE_EQUATION are INLINE_EQUATION and INLINE_EQUATION,
-respectively. Both INLINE_EQUATION and INLINE_EQUATION can
+option, the dimensions of :math:`G` and :math:`D` are :math:`N_{chan} \times N_{source}` and :math:`N_{chan} \times 3N_{source}`,
+respectively. Both :math:`G` and :math:`D` can
be read with the mne_read_forward_solution Matlab
function, see Table 10.1.
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