[med-svn] [python-mne] 181/376: fixing manual

[Yaroslav Halchenko]

This is an automated email from the git hooks/post-receive script.

yoh pushed a commit to annotated tag v0.1
in repository python-mne.

commit 700c4bd173e4ee088185d454c5f31c6d70596cca
Author: Emily Ruzich <emilyr at nmr.mgh.harvard.edu>
Date:   Fri Apr 1 11:50:16 2011 -0400

    fixing manual
---
 doc/source/manual/AppA.rst            |  4 ++--
 doc/source/manual/AppReleaseNotes.rst |  4 ++--
 doc/source/manual/cookbook.rst        | 11 +++++++++--
 3 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/doc/source/manual/AppA.rst b/doc/source/manual/AppA.rst
index ac4f09b..b730f3d 100755
--- a/doc/source/manual/AppA.rst
+++ b/doc/source/manual/AppA.rst
@@ -234,8 +234,8 @@ Inspecting the meshes
 
 It is advisable to check the validity of the BEM meshes before
 using them. This can be done with help of tkmedit either
-before or after executing mne_setup_forward_model ,
-see Section 3.7.
+before or after executing mne_setup_forward_model,
+see :ref:`CIHDBFEG`.
 
 Using seglab
 ############
diff --git a/doc/source/manual/AppReleaseNotes.rst b/doc/source/manual/AppReleaseNotes.rst
index f20249f..eb76545 100755
--- a/doc/source/manual/AppReleaseNotes.rst
+++ b/doc/source/manual/AppReleaseNotes.rst
@@ -654,7 +654,7 @@ mne_opengl_test
 ---------------
 
 New utility for testing the OpenGL graphics performance,
-see Section C.2.5.
+see :ref:`CIHIIBDA`.
 
 mne_volume_data2mri
 -------------------
@@ -846,7 +846,7 @@ Miscellaneous
   see :ref:`CBBBBHIF`.
 
 - Added --noiserank option to mne_inverse_operator and mne_do_inverse_operator ,
-  see :ref:`CBBDDBGF`and Section 3.13, respectively.
+  see :ref:`CBBDDBGF`and :ref:`CIHCFJEI`, respectively.
 
 - The fif output from mne_convert_dig_data now
   includes the transformation between the digitizer and MNE head coordinate
diff --git a/doc/source/manual/cookbook.rst b/doc/source/manual/cookbook.rst
index 5c44d1a..14282a9 100755
--- a/doc/source/manual/cookbook.rst
+++ b/doc/source/manual/cookbook.rst
@@ -815,10 +815,17 @@ anatomy only, not on the MEG/EEG data to be analyzed.
 
 .. note:: The MEG head to MRI transformation matrix specified    with the ``--trans`` option should be a text file containing    a 4-by-4 matrix:
 
-.. math::    1 + 1 = 2
+.. math::    T = \[
+		\begin{matrix}
+		R_11 & R_12 & R_13 x_0 \\
+		R_13 & R_13 & R_13 y_0 \\
+		R_13 & R_13 & R_13 z_0 \\
+		0 & 0 & 0 & 1 \\
+		\end{matrix}
+		\]
 
 defined so that if the augmented location vectors in MRI
-head and MRI coordinate systems are denoted by INLINE_EQUATION and :math:`r_{head}[x_{MRI}\ y_{MRI}\ z_{MRI}\ 1]`,
+head and MRI coordinate systems are denoted by :math:`r_{head}[x_{head}\ y_{head}\ z_{head}\ 1]` and :math:`r_{MRI}[x_{MRI}\ y_{MRI}\ z_{MRI}\ 1]`,
 respectively,
 
 .. math::    r_{MRI} = T r_{head}

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git