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fixing manual
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emilyruzich committed Mar 21, 2011
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12 changes: 6 additions & 6 deletions doc/source/manual/analyze.rst
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Expand Up @@ -936,7 +936,7 @@ includes the following lines:
Shows the location in the *FreeSurfer* Talairach
coordinates which give a better match to the Talairach atlas.

The above coordinate systems are discussed in detail in Section 5.2.
The above coordinate systems are discussed in detail in :ref:`CHDEDFIB`.

.. note:: By default, the tksurfer program, part of the FreeSurfer package, shows the vertex locations on the *orig* rather than *white* surfaces. Therefore, the coordinates shown in mne_analyze and tksurfer are by default slightly different (usually by < 1 mm). To make the two programs consistent, you can start tksurfer with the ``-orig white`` option.

Expand Down Expand Up @@ -1176,13 +1176,13 @@ the subject's FreeSurfer directory. This surface is automatically
prepared if you use the watershed algorithm as described in Section A.1.
If you have another source for the head triangulation you can use
the utility mne_surf2bem to create
the fif format scalp surface file, see Section 5.6.
the fif format scalp surface file, see :ref:`BEHCACCJ`.

If a file called ``bem/`` <subject>``-bem.fif`` under
the subject's FreeSurfer directory is present, mne_analyze tries
to load the BEM surface triangulations from there. This file can
be a symbolic link to one of the ``-bem.files`` created
by mne_prepare_bem_model , see Section 5.7.
by mne_prepare_bem_model , see :ref:`CHDJFHEB`.
If the BEM file contains a head surface triangulation, it will be
used instead of the one present in the ``bem/`` <subject>``-head.fif`` file.

Expand Down Expand Up @@ -1984,12 +1984,12 @@ specifies the forward model to be used:
**EEG scalp radius [mm]**

Specifies the radius of the outermost shell in the EEG sphere model. For
details, see Section 5.9.4.
details, see :ref:`CHDIAFIG`.

**EEG sphere model name**

Specifies the name of the EEG sphere model to use. For details,
see Section 5.9.4.
see :ref:`CHDIAFIG`.

**BEM model**

Expand All @@ -2002,7 +2002,7 @@ specifies the forward model to be used:

**Accurate field calculation**

Switches on the more accurate geometry definition of MEG coils, see Section 5.8.
Switches on the more accurate geometry definition of MEG coils, see :ref:`BJEIAEIE`.
In dipole fitting, there is very little difference between the *accurate* and *normal* coil
geometry definitions.

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8 changes: 4 additions & 4 deletions doc/source/manual/convert.rst
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Expand Up @@ -991,7 +991,7 @@ Converting volumetric data into an MRI overlay
##############################################

With help of the mne_volume_source_space utility
(Section 5.5) it is possible to create a source space which
(:ref:`BJEFEHJI`) it is possible to create a source space which
is defined within a volume rather than a surface. If the ``--mri`` option
was used in mne_volume_source_space , the
source space file contains an interpolator matrix which performs
Expand Down Expand Up @@ -1207,7 +1207,7 @@ the following command-line options:

**\---tri <name>**

Specifies a text format input file. The format of this file is described in Section 5.6.3.
Specifies a text format input file. The format of this file is described in :ref:`BEHDEFCD`.

**\---meters**

Expand Down Expand Up @@ -1295,7 +1295,7 @@ the following command-line options:
**\---triout <name>**

Specifies an ASCII output file that will contain the surface data
in the triangle file format desribed in Section 5.6.3.
in the triangle file format desribed in :ref:`BEHDEFCD`.

**\---pntout <name>**

Expand Down Expand Up @@ -1367,7 +1367,7 @@ data as input. The command-line options are:
the talairach.xfm file referred to in the MRI volume, and the the
fixed transforms INLINE_EQUATION and INLINE_EQUATION will
added to the output file. For definition of the coordinate transformations,
see Section 5.2.
see :ref:`CHDEDFIB`.

**\---talairach <name>**

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24 changes: 12 additions & 12 deletions doc/source/manual/list.rst
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Expand Up @@ -36,7 +36,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_compute_mne* | Computes the minimum-norm estimates, |
| | see Section B.3.1. Most of the |
| | functionality of mne_compute_mne is |
| | included in mne_make_movie. |
| | included in mne_make_movie. |
+----------------------------+--------------------------------------------+
| *mne_compute_raw_inverse* | Compute the inverse solution from raw data |
| | see :ref:`CBBCGHAH`. |
Expand All @@ -47,11 +47,11 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_do_forward_solution* | Convenience script to calculate the forward|
| | solution matrix, see :ref:`BABCHEJD`. |
+----------------------------+--------------------------------------------+
| *mne_do_inverse_operator* | Convenience script to compute the inverse |
| | operator decomposition, see :ref:`CIHCFJEI`.|
| *mne_do_inverse_operator* | Convenience script for inverse operator |
| | decomposition, see :ref:`CIHCFJEI`. |
+----------------------------+--------------------------------------------+
| *mne_forward_solution* | Calculate the forward solution matrix, see |
| | Section 5.9. |
| | :ref:`CHDDIBAH`. |
+----------------------------+--------------------------------------------+
| mne_inverse_operator | Compute the inverse operator decomposition |
| | see Section 6.4. |
Expand All @@ -60,7 +60,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | :ref:`CBBECEDE`. |
+----------------------------+--------------------------------------------+
| *mne_make_source_space* | Create a *fif* source space description |
| | file, see Section 5.4. |
| | file, see :ref:`BEHCGJDD`. |
+----------------------------+--------------------------------------------+
| *mne_process_raw* | A batch-mode version of mne_browse_raw, |
| | see :ref:`ch_browse`. |
Expand Down Expand Up @@ -120,7 +120,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | fif data file, see :ref:`CHDIJHIC`. |
+---------------------------------+--------------------------------------------+
| *mne_average_forward_solutions* | Calculate an average of forward solutions, |
| | see Section 5.10. |
| | see :ref:`CHDBBFCA`. |
+---------------------------------+--------------------------------------------+
| *mne_brain_vision2fiff* | Convert EEG data from BrainVision format |
| | to fif format, see Section 9.2.10. |
Expand Down Expand Up @@ -196,8 +196,8 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_eximia2fiff* | Convert EEG data from the Nexstim eXimia |
| | system to fif format, see Section 9.2.11. |
+---------------------------------+--------------------------------------------+
| *mne_fit_sphere_to_surf* | Fit a sphere to a surface given in either |
| | fif or FreeSurfer format, see :ref:`CHDECHBF`.|
| *mne_fit_sphere_to_surf* | Fit a sphere to a surface given in fif |
| | or FreeSurfer format, see :ref:`CHDECHBF`. |
+---------------------------------+--------------------------------------------+
| *mne_fix_mag_coil_types* | Update the coil types for magnetometers |
| | in a fif file, see :ref:`CHDGAAJC`. |
Expand All @@ -218,7 +218,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
+---------------------------------+--------------------------------------------+
| *mne_list_coil_def* | Create the coil description file. This |
| | is run automatically at when the software |
| | is set up, see Section 5.8.5. |
| | is set up, see :ref:`BJEHHJIJ`. |
+---------------------------------+--------------------------------------------+
| *mne_list_proj* | List signal-space projection data from a |
| | fif file. |
Expand Down Expand Up @@ -260,7 +260,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | directories, see Section A.2.1. |
+---------------------------------+--------------------------------------------+
| *mne_prepare_bem_model* | Perform the geometry calculations for |
| | BEM forward solutions, see Section 5.7. |
| | BEM forward solutions, see :ref:`CHDJFHEB`.|
+---------------------------------+--------------------------------------------+
| mne_process_stc | Manipulate stc files. |
+---------------------------------+--------------------------------------------+
Expand Down Expand Up @@ -288,7 +288,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| *mne_surf2bem* | Create a *fif* file describing the |
| | triangulated compartment boundaries for |
| | the boundary-element model (BEM), |
| | see Section 5.6. |
| | see :ref:`BEHCACCJ`. |
+---------------------------------+--------------------------------------------+
| *mne_toggle_skips* | Change data skip tags in a raw file into |
| | ignored skips or vice versa. |
Expand All @@ -309,7 +309,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
| | overlay, see Section 9.4. |
+---------------------------------+--------------------------------------------+
| *mne_volume_source_space* | Make a volumetric source space, |
| | see Section 5.5. |
| | see :ref:`BJEFEHJI`. |
+---------------------------------+--------------------------------------------+
| *mne_watershed_bem* | Do the segmentation for BEM using the |
| | watershed algorithm, see Section A.1. |
Expand Down
6 changes: 3 additions & 3 deletions doc/source/manual/matlab.rst
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Expand Up @@ -312,7 +312,7 @@ The documented structures are:

The coil definition structure useful for forward calculations and array
visualization, see :ref:`BGBGBEBH`. For more detailed information on
coil definitions, see Section 5.8.
coil definitions, see :ref:`BJEIAEIE`.

**ch**

Expand Down Expand Up @@ -523,7 +523,7 @@ The documented structures are:

.. _BGBGBEBH:

.. table:: The coildef structure. For more detailed information, see Section 5.8.
.. table:: The coildef structure. For more detailed information, see :ref:`BJEIAEIE`.

============== ======================= ========================================================================================
Field Data type Description
Expand Down Expand Up @@ -677,7 +677,7 @@ The documented structures are:
nsource int32 Total number of source space points.
nchan int32 Number of channels.
sol named matrix The forward solution matrix.
sol_grad named matrix The derivatives of the forward solution with respect to the dipole location coordinates, see Section 5.9.6. This field is present only if the forward solution was computed with the ``--grad`` option, see Section 5.9.2.
sol_grad named matrix The derivatives of the forward solution with respect to the dipole location coordinates, see :ref:`BJEFEJJG`. This field is present only if the forward solution was computed with the ``--grad`` option, see :ref:`BJEIGFAE`.
mri_head_t trans Transformation from the MRI coordinate frame to the (Neuromag) head coordinate frame.
src surf(*) The description of the source spaces
source_rr double(nsource,3) The source locations.
Expand Down

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