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commit 0c1e6d9baa7ce2f1737616fabf7dac0c1770718c Author: Emily Ruzich <[email protected]> Date: Wed Mar 23 15:56:26 2011 -0400 fixing manual --- doc/source/manual/browse.rst | 4 ++-- doc/source/manual/forward.rst | 6 +++--- doc/source/manual/list.rst | 20 ++++++++++---------- doc/source/manual/matlab.rst | 2 +- doc/source/manual/mne.rst | 2 +- doc/source/manual/morph.rst | 2 +- 6 files changed, 18 insertions(+), 18 deletions(-) diff --git a/doc/source/manual/browse.rst b/doc/source/manual/browse.rst index 28a33f6..306b4b8 100644 --- a/doc/source/manual/browse.rst +++ b/doc/source/manual/browse.rst @@ -455,7 +455,7 @@ selection affects the averages and noise-covariance matrices subsequently computed. The desired compensation takes effect independent of the compensation state of the data in the file, *i.e.*, already compensated data can be uncompensated and vice versa. For more -information on software gradient compensation please consult Section 9.2.4. +information on software gradient compensation please consult :ref:`BEHDDFBI`. The Keep the initial skip button controls how the initial segment of data not stored in the raw data @@ -1614,7 +1614,7 @@ an annotation file which will be automatically loaded each time the data file is opened. A text format event file suitable for this purpose can be created manually, extracted from an EDF+ file using the ``--tal`` option in mne_edf2fiff discussed -in Section 9.2.8, or produced by custom software used during +in :ref:`BABHDBBD`, or produced by custom software used during data acquisition. .. _BABCIGGH: diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst index 14b9665..08803fb 100644 --- a/doc/source/manual/forward.rst +++ b/doc/source/manual/forward.rst @@ -191,7 +191,7 @@ and INLINE_EQUATION axis pointing front. The INLINE_EQUATION axis is, again normal to the INLINE_EQUATION plane with positive direction up. -.. note:: The above definition is identical to that of the Neuromag MEG/EEG (head) coordinate system. However, in 4-D Neuroimaging and CTF MEG systems the head coordinate frame definition is different. The origin of the coordinate system is at the midpoint of the left and right auricular points. The INLINE_EQUATION axis passes through the nasion and the origin with positive direction to the front. The INLINE_EQUATION axis is perpendicular to the INLINE_EQUATION axis [...] +.. note:: The above definition is identical to that of the Neuromag MEG/EEG (head) coordinate system. However, in 4-D Neuroimaging and CTF MEG systems the head coordinate frame definition is different. The origin of the coordinate system is at the midpoint of the left and right auricular points. The INLINE_EQUATION axis passes through the nasion and the origin with positive direction to the front. The INLINE_EQUATION axis is perpendicular to the INLINE_EQUATION axis [...] .. _BEHCGJDD: @@ -1098,7 +1098,7 @@ the following command-line options: Implementation of software gradient compensation ================================================ -As described in Section 9.2.4 the CTF and 4D Neuroimaging +As described in :ref:`BEHDDFBI` the CTF and 4D Neuroimaging data may have been subjected to noise cancellation employing the data from the reference sensor array. Even though these sensor are rather far away from the brain sources, mne_forward_solution takes @@ -1107,7 +1107,7 @@ with the ``--meas`` option has software gradient compensation activated, mne_forward_solution computes the field of at the reference sensors in addition to the main MEG sensor array and computes a compensated forward solution using the -methods descibed in Section 9.2.4. +methods descibed in :ref:`BEHDDFBI`. .. warning:: If a data file specified with the ``--meas`` option and that used in the actual inverse computations with mne_analyze and mne_make_movie have different software gradient compensation states., the forward solution will be in mismatch with the data to be analyzed and the current estimates will be slightly erroneous. diff --git a/doc/source/manual/list.rst b/doc/source/manual/list.rst index 5ec9ce3..88f5a98 100644 --- a/doc/source/manual/list.rst +++ b/doc/source/manual/list.rst @@ -26,7 +26,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities. | | :ref:`ch_interactive_analysis`. | +----------------------------+--------------------------------------------+ | *mne_average_estimates* | Average data across subjects, | - | | see Section 8.6.2. | + | | see :ref:`CHDEHFGD`. | +----------------------------+--------------------------------------------+ | *mne_browse_raw* | Interactive raw data browser. Includes | | | filtering, offline averaging, and | @@ -150,7 +150,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities. +---------------------------------+--------------------------------------------+ | *mne_compensate_data* | Change the applied software gradient | | | compensation in an evoked-response data | - | | file, see Section 9.2.4. | + | | file, see :ref:`BEHDDFBI`. | +---------------------------------+--------------------------------------------+ | *mne_convert_lspcov* | Convert the LISP format noise covariance | | | matrix output by graph into fif, | @@ -169,13 +169,13 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities. +---------------------------------+--------------------------------------------+ | *mne_create_comp_data* | Create a fif file containing software | | | gradient compensation information from a | - | | text file, see Section 9.2.6. | + | | text file, see :ref:`BEHBIIFF`. | +---------------------------------+--------------------------------------------+ | *mne_ctf2fiff* | Convert a CTF ds folder into a fif file, | - | | see Section 9.2.2. | + | | see :ref:`BEHDEBCH`. | +---------------------------------+--------------------------------------------+ | *mne_ctf_dig2fiff* | Convert text format digitization data to | - | | fif format, see Section 9.2.3. | + | | fif format, see :ref:`BEHBABFA`. | +---------------------------------+--------------------------------------------+ | *mne_dicom_essentials* | List essential information from a | | | DICOM file. | @@ -184,7 +184,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities. +---------------------------------+--------------------------------------------+ | *mne_edf2fiff* | Convert EEG data from the EDF/EDF+/BDF | | | formats to the fif format, | - | | see Section 9.2. | + | | see :ref:`BEHIAADG`. | +---------------------------------+--------------------------------------------+ | *mne_epochs2mat* | Apply bandpass filter to raw data and | | | extract epochs for subsequent processing | @@ -194,7 +194,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities. | | file to the standard output. | +---------------------------------+--------------------------------------------+ | *mne_eximia2fiff* | Convert EEG data from the Nexstim eXimia | - | | system to fif format, see Section 9.2.11. | + | | system to fif format, see :ref:`BEHGCEHH`. | +---------------------------------+--------------------------------------------+ | *mne_fit_sphere_to_surf* | Fit a sphere to a surface given in fif | | | or FreeSurfer format, see :ref:`CHDECHBF`. | @@ -211,7 +211,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities. | *mne_insert_4D_comp* | Read Magnes compensation channel data from | | | a text file and merge it with raw data | | | from other channels in a fif file, see | - | | Section 9.2.5. | + | | :ref:`BEHGDDBH`. | +---------------------------------+--------------------------------------------+ | *mne_list_bem* | List BEM information in text format, | | | see Section 9.6. | @@ -254,7 +254,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities. | | a data file, see :ref:`CHDDHBEE`. | +---------------------------------+--------------------------------------------+ | *mne_morph_labels* | Morph label file definitions between | - | | subjects, see Section 8.5. | + | | subjects, see :ref:`CHDCEAFC`. | +---------------------------------+--------------------------------------------+ | *mne_organize_dicom* | Organized DICOM MRI image files into | | | directories, see Section A.2.1. | @@ -298,7 +298,7 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities. +---------------------------------+--------------------------------------------+ | *mne_tufts2fiff* | Convert EEG data from the Tufts | | | University format to fif format, | - | | see Section 9.2.9. | + | | see :ref:`BEHDGAIJ`. | +---------------------------------+--------------------------------------------+ | *mne_view_manual* | Starts a PDF reader to show this manual | | | from its standard location. | diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst index 054073f..1ce91e6 100644 --- a/doc/source/manual/matlab.rst +++ b/doc/source/manual/matlab.rst @@ -585,7 +585,7 @@ The documented structures are: save_calibrated logical Were the compensation data saved in calibrated form. If this field is false, the matrix will be decalibrated using the fields row_cals and col_cals when the compensation data are saved by the toolbox. row_cals double(*) Calibration factors applied to the rows of the compensation data matrix when the data were read. col_cals double(*) Calibration factors applied to the columns of the compensation data matrix when the data were read. - data named matrix The compensation data matrix. The row_names list the names of the channels to which this compensation applies and the col_names the compensation channels. For more information, see Section 9.2.4 + data named matrix The compensation data matrix. The row_names list the names of the channels to which this compensation applies and the col_names the compensation channels. For more information, see :ref:`BEHDDFBI`. ================== =============== =========================================================================================================================================================================================================== .. _BGBFHDIJ: diff --git a/doc/source/manual/mne.rst b/doc/source/manual/mne.rst index d7325ef..ab4d8f9 100644 --- a/doc/source/manual/mne.rst +++ b/doc/source/manual/mne.rst @@ -808,7 +808,7 @@ Visualization options into account and will represent the data on the cortical surface of the subject defined with this option. The stc files morphed to a single subject's cortical surface are used by mne_average_estimates to - combine data from different subjects, see Section 8.6. + combine data from different subjects, see :ref:`CHDFDIFE`. If morphing is selected appropriate smoothing must be specified with the ``--smooth`` option. The morphing process can be made faster by precomputing the necessary morphing maps with mne_make_morph_maps , diff --git a/doc/source/manual/morph.rst b/doc/source/manual/morph.rst index 082e22c..2ce04a8 100644 --- a/doc/source/manual/morph.rst +++ b/doc/source/manual/morph.rst @@ -29,7 +29,7 @@ maps which can be either computed on demand or precomputed using mne_make_morph_ see :ref:`CHDBBHDH`. The morphing is performed with help of the registered spherical surfaces (``lh.sphere.reg`` and ``rh.sphere.reg`` ) which must be produced in FreeSurfer . -A morphing map is a linear mapping from cortical surface values +A morphing map is a linear mapping froprem cortical surface values in subject A (INLINE_EQUATION) to those in another subject B (INLINE_EQUATION) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
