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commit c6570a2d252be0067f7b170548799b1dcb2167e2 Author: Alexandre Gramfort <[email protected]> Date: Thu Mar 3 16:40:21 2011 -0500 more on doc --- doc/source/manual/analyze.rst | 34 ++++++------- doc/source/manual/browse.rst | 12 +++++ doc/source/manual/convert.rst | 8 ++-- doc/source/manual/forward.rst | 103 ++++++++++++++++++++++++++++------------ doc/source/manual/matlab.rst | 55 +++++++++++---------- doc/source/manual/utilities.rst | 8 ++-- 6 files changed, 140 insertions(+), 80 deletions(-) diff --git a/doc/source/manual/analyze.rst b/doc/source/manual/analyze.rst index e9c96ed..405dfba 100644 --- a/doc/source/manual/analyze.rst +++ b/doc/source/manual/analyze.rst @@ -176,8 +176,10 @@ The File shown in :ref:`CACJCBFI` contains the following items: .. figure:: mne_analyze/file_menu.png :alt: the file menu + :align: center + :figwidth: 25% - The File menu. + The file menu **Open...** @@ -646,11 +648,11 @@ which is invoked by selecting Adjust/Scales... from the menus. The Scales dialog shown in :ref:`CACJJCGD` has the following entries: -**Analyze range min\s]** +**Analyze range min [ms]** Specifies the lower limit of the time range of data to be shown. -**Analyze range max\s]** +**Analyze range max [ms]** Specifies the upper limit of the time range of data to be shown. @@ -659,11 +661,11 @@ shown in :ref:`CACJJCGD` has the following entries: If this box is checked, all data available in the data file will be shown. -**Baseline min\s]** +**Baseline min [ms]** Specifies the lower time limit of the baseline. -**Baseline max\s]** +**Baseline max [ms]** Specifies the upper time limit of the baseline. @@ -671,25 +673,25 @@ shown in :ref:`CACJJCGD` has the following entries: Baseline subtraction can be switched on and off from this button. -**MEG amp min\T/cm]** +**MEG amp min [fT/cm]** Lower limit of the vertical scale of planar gradiometer MEG channels. -**MEG amp max\T/cm]** +**MEG amp max [fT/cm]** Upper limit of the vertical scale of planar gradiometer MEG channels. -**MEG axmult\m]** +**MEG axmult [cm]** The vertical scale of MEG magnetometers and axial gradiometers will be obtained by multiplying the planar gradiometer vertical scale limits by this value, given in centimeters. -**EEG amp min [INLINE_EQUATIONV]** +**EEG amp min [muV]** Lower limit of the vertical scale of EEG channels. -**EEG amp max [INLINE_EQUATIONV]** +**EEG amp max [muV]** Upper limit of the vertical scale of EEG channels. @@ -1596,7 +1598,7 @@ controls: | fthresh | If the value is below this level, it will not be shown. | +------------+---------------------------------------------------------+ | fmid | Positive values at this level will show as red. | - | Negative values will be dark blue. | + | | Negative values will be dark blue. | +------------+---------------------------------------------------------+ | fmax | Positive values at and above this level will be bright | | | yellow. Negative values will be bright blue. | @@ -1974,12 +1976,12 @@ and Noise estimate . The Forward model section specifies the forward model to be used: -**Sphere model origin x/y/z\m]** +**Sphere model origin x/y/z [mm]** Specifies the origin of the spherically symmetric conductor model in MEG/EEG head coordinates, see :ref:`BJEBIBAI`. -**EEG scalp radius\m]** +**EEG scalp radius [mm]** Specifies the radius of the outermost shell in the EEG sphere model. For details, see Section 5.9.4. @@ -2036,19 +2038,19 @@ of the dialog contains the following items: EEG is included in fitting it is advisable to enter a non-zero value (around 0.1) here. -**Planar fixed\T/cm]** +**Planar fixed [fT/cm]** In the absense of a noise covariance matrix selection, a diagonal noise covariance with fixed values on the diagonal is used. This entry specifies the fixed value of the planar gradiometers. -**Axial fixed\T]** +**Axial fixed [fT]** If a noise covariance matrix file is not specified, this entry specifies a fixed diagonal noise covariance matrix value for axial gradiometers and magnetometers. -**EEG fixed [INLINE_EQUATIONV]** +**EEG fixed [muV]** If a noise covariance matrix file is not specified, this entry specifies a fixed diagonal noise covariance matrix value for axial gradiometers diff --git a/doc/source/manual/browse.rst b/doc/source/manual/browse.rst index d8a7c7f..37dfba4 100644 --- a/doc/source/manual/browse.rst +++ b/doc/source/manual/browse.rst @@ -410,6 +410,8 @@ The user interface .. figure:: mne_browse_raw/windows_menu-7.png :alt: The user interface of mne_browse_raw + :figwidth: 100% + :width: 100% The user interface of mne_browse_raw @@ -666,6 +668,9 @@ shown in :ref:`CACCEEGI`. .. figure:: mne_browse_raw/filter_dialog.png :alt: filter adjustment dialog + :align: center + :figwidth: 55% + :width: 400 The filter adjustment dialog. @@ -716,6 +721,8 @@ shown in :ref:`CACBJGBA`. .. figure:: mne_browse_raw/scales_dialog.png :alt: Scales dialog + :figwidth: 100% + :width: 100% The Scales dialog. @@ -1084,10 +1091,13 @@ This overrides the choice made at the open time. For details, see :ref:`CACDCHAJ Averaging preferences ===================== + .. _CACCFFAH: .. figure:: mne_browse_raw/average_pref.png :alt: Averaging preferences + :figwidth: 35% + :width: 300 Averaging preferences. @@ -1699,6 +1709,8 @@ The tool bar .. figure:: mne_browse_raw/toolbar.png :alt: tool bar controls + :figwidth: 100% + :width: 100% The tool bar controls. diff --git a/doc/source/manual/convert.rst b/doc/source/manual/convert.rst index 3bd46db..65c775b 100644 --- a/doc/source/manual/convert.rst +++ b/doc/source/manual/convert.rst @@ -1071,15 +1071,15 @@ The command-line options are: **\---src <name>** The source space to be listed. This can be either the output from mne_make_source_space - \src.fif), output from the forward calculation \fwd.fif), or - the output from the inverse operator decomposition \inv.fif). + (*src.fif), output from the forward calculation (*fwd.fif), or + the output from the inverse operator decomposition (*inv.fif). **\---mri <name>** A file containing the transformation between the head and MRI coordinates is specified with this option. This file can be either a Neuromag - MRI description file, the output from the forward calculation \fwd.fif), - or the output from the inverse operator decomposition \inv.fif). + MRI description file, the output from the forward calculation (*fwd.fif), + or the output from the inverse operator decomposition (*inv.fif). If this file is included, the output will be in head coordinates. Otherwise the source space will be listed in MRI coordinates. diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst index e9a547a..c0a3bd9 100644 --- a/doc/source/manual/forward.rst +++ b/doc/source/manual/forward.rst @@ -33,7 +33,7 @@ to the front, and the INLINE_EQUATION axis up. :alt: MEG/EEG and MRI coordinate systems MEG/EEG and MRI coordinate systems - + The coordinate transforms present in the fif files in MNE and the FreeSurfer files as well as those set to fixed values are indicated with INLINE_EQUATION, where INLINE_EQUATION identifies the transformation. The coordinate systems related @@ -144,15 +144,16 @@ and .. _CHDJDEDJ: +.. tabularcolumns:: |p{0.2\linewidth}|p{0.3\linewidth}||p{0.5\linewidth}| .. table:: Coordinate transformations in FreeSurfer and MNE software packages. The symbols INLINE_EQUATION are defined in :ref:`CHDFFJIJ` Note: mne_make_cor_set /mne_setup_mri prior to release 2.6 did not include transformations INLINE_EQUATION, INLINE_EQUATION, INLINE_EQUATION, and INLINE_EQUATION in the fif files produced.). ================== =============================== ======================================================================================================================================= Transformation FreeSurfer MNE ================== =============================== ======================================================================================================================================= - INLINE_EQUATION Not present Measurement data files Forward solution files \fwd.fif) Inverse operator files \inv.fif) + INLINE_EQUATION Not present Measurement data files Forward solution files (*fwd.fif) Inverse operator files (*inv.fif) INLINE_EQUATION Not present Channel information in files containing INLINE_EQUATION. INLINE_EQUATION Not present MRI description files Separate coordinate transformation files saved from mne_analyze Forward solution files Inverse operator files - INLINE_EQUATION mri\mgz files MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format. + INLINE_EQUATION mri/*mgz files MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format. INLINE_EQUATION mri/transforms/talairach.xfm MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format. INLINE_EQUATION Hardcoded in software MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format. INLINE_EQUATION Hardcoded in software MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format. @@ -730,6 +731,7 @@ The columns of the tables contain the following data: .. _BGBBHGEC: +.. tabularcolumns:: |p{0.1\linewidth}|p{0.3\linewidth}|p{0.1\linewidth}|p{0.3\linewidth}|p{0.2\linewidth}| .. table:: Normal coil descriptions. Note: If a plus-minus sign occurs in several coordinates, all possible combinations have to be included. ======= ================================================================ ==== =============================================================== =============================================================== @@ -744,42 +746,80 @@ The columns of the tables contain the following data: 3024 Vectorview type 3 magnetometer 4 INLINE_EQUATION INLINE_EQUATION 2000 An ideal point magnetometer 1 (0,0,0) 1 4001 Magnes WH magnetometer 4 INLINE_EQUATION INLINE_EQUATION - 4002 Magnes WH 3600 axial gradiometer 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION + 4002 Magnes WH 3600 axial gradiometer 8 INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION 4003 Magnes reference magnetometer 4 INLINE_EQUATION INLINE_EQUATION - 4004 Magnes reference gradiometer measuring diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION - 4005 Magnes reference gradiometer measuring off-diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION - 5001 CTF 275 axial gradiometer 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION + 4004 Magnes reference gradiometer measuring diagonal gradients 8 INLINE_EQUATION 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_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION - 5004 CTF reference gradiometer measuring off-diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION - 6001 MIT KIT system axial gradiometer 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_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 ======= ================================================================ ==== =============================================================== =============================================================== .. _CHDBDFJE: +.. XXX : incomplete + +.. tabularcolumns:: |p{0.1\linewidth}|p{0.3\linewidth}|p{0.1\linewidth}|p{0.25\linewidth}|p{0.2\linewidth}| .. table:: Accurate coil descriptions - ======= ================================================================ ===== ============================================================================================= ============================================================================================= - Id Description n r/mm w - ======= ================================================================ ===== ============================================================================================= ============================================================================================= - 2 Neuromag-122 planar gradiometer 8 INLINE_EQUATION,INLINE_EQUATION INLINE_EQUATION - 2000 A point magnetometer 1 INLINE_EQUATION 1 - 3012 Vectorview type 1 planar gradiometer 8 INLINE_EQUATION,INLINE_EQUATION INLINE_EQUATION - 3013 Vectorview type 2 planar gradiometer 8 INLINE_EQUATION,INLINE_EQUATION INLINE_EQUATION - 3022 Vectorview type 1 magnetometer 16 INLINE_EQUATION,INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATION - 3023 Vectorview type 2 magnetometer 16 INLINE_EQUATION,INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATION - 3024 Vectorview type 3 magnetometer 16 INLINE_EQUATION,INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATION - 4001 Magnes WH magnetometer 7 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION - 4002 Magnes WH 3600 axial gradiometer 14 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION - 4004 Magnes reference gradiometer measuring diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION - 4005 Magnes reference gradiometer measuring off-diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION - 4004 Magnes reference gradiometer measuring diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION - 5001 CTF 275 axial gradiometer 14 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION - 5002 CTF reference magnetometer 4 INLINE_EQUATION INLINE_EQUATION - 5003 CTF reference gradiometer measuring diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION - 5004 CTF reference gradiometer measuring off-diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION - 6001 MIT KIT system axial gradiometer 14 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION - ======= ================================================================ ===== ============================================================================================= ============================================================================================= + +------+-------------------------+----+----------------------------------+----------------------+ + | Id | Description | n | r/mm | w | + +======+=========================+====+==================================+======================+ + | 2 | Neuromag-122 planar | 8 | +/-(8.1, 0, 0) mm | +/-1 ⁄ 16.2mm | + | | gradiometer | | | | + +------+-------------------------+----+----------------------------------+----------------------+ + | 2000 | A point magnetometer | 1 | (0, 0, 0) mm | 1 | + +------+-------------------------+----+----------------------------------+----------------------+ + | 3012 | Vectorview type 1 | 2 | (+/-8.4, 0, 0.3) mm | +/-1 ⁄ 16.8mm | + | | planar gradiometer | | | | + +------+-------------------------+----+----------------------------------+----------------------+ + | 3013 | Vectorview type 2 | 2 | (+/-8.4, 0, 0.3) mm | +/-1 ⁄ 16.8mm | + | | planar gradiometer | | | | + +------+-------------------------+----+----------------------------------+----------------------+ + | 3022 | Vectorview type 1 | 4 | (+/-6.45, +/-6.45, 0.3)mm | 1/4 | + | | magnetometer | | | | + +------+-------------------------+----+----------------------------------+----------------------+ + | 3023 | Vectorview type 2 | 4 | (+/-6.45, +/-6.45, 0.3)mm | 1/4 | + | | magnetometer | | | | + +------+-------------------------+----+----------------------------------+----------------------+ + | 3024 | Vectorview type 3 | 4 | (+/-5.25, +/-5.25, 0.3)mm | 1/4 | + | | magnetometer | | | | + +------+-------------------------+----+----------------------------------+----------------------+ + | 4001 | Magnes WH magnetometer | 4 | (+/-5.75, +/-5.75, 0.0)mm | 1/4 | + +------+-------------------------+----+----------------------------------+----------------------+ + | 4002 | Magnes WH 3600 | 4 | (+/-4.5, +/-4.5, 0.0)mm | 1/4 | + | | axial gradiometer | | (+/-4.5, +/-4.5, 0.0)mm | -1/4 | + +------+-------------------------+----+----------------------------------+----------------------+ + | 4004 | Magnes reference | 8 | (+/-20, +/-20, 0.0)mm | 1/4 | + | | gradiometer measuring | | (+/-20, +/-20, 135)mm | -1/4 | + | | diagonal gradients | | | | + +------+-------------------------+----+----------------------------------+----------------------+ + | 4005 | Magnes reference | 8 | (87.5, +/-20, 0.0)mm | 1/4 | + | | gradiometer measuring | | (47.5, +/-20, 0.0)mm | -1/4 | + | | off-diagonal gradients | | (-87.5, +/-20, 0.0)mm | 1/4 | + | | | | (-47.5, +/-20, 0.0)mm | -1/4 | + +------+-------------------------+----+----------------------------------+----------------------+ + | 5001 | CTF 275 axial | 8 | (+/-4.5, +/-4.5, 0.0)mm | 1/4 | + | | gradiometer | | (+/-4.5, +/-4.5, 50.0)mm | -1/4 | + +------+-------------------------+----+----------------------------------+----------------------+ + | 5002 | CTF reference | 4 | (+/-4, +/-4, 0.0)mm | 1/4 | + | | magnetometer | | | | + +------+-------------------------+----+----------------------------------+----------------------+ + | 5003 | CTF 275 reference | 8 | (+/-8.6, +/-8.6, 0.0)mm | 1/4 | + | | gradiometer measuring | | (+/-8.6, +/-8.6, 78.6)mm | -1/4 | + | | diagonal gradients | | | | + +------+-------------------------+----+----------------------------------+----------------------+ + | 5004 | CTF 275 reference | 8 | (47.8, +/-8.5, 0.0)mm | 1/4 | + | | gradiometer measuring | | (30.8, +/-8.5, 0.0)mm | -1/4 | + | | off-diagonal gradients | | (-47.8, +/-8.5, 0.0)mm | 1/4 | + | | | | (-30.8, +/-8.5, 0.0)mm | -1/4 | + +------+-------------------------+----+----------------------------------+----------------------+ + | 6001 | MIT KIT system axial | 8 | (+/-3.875, +/-3.875, 0.0)mm | 1/4 | + | | gradiometer | | (+/-3.875, +/-3.875, 0.0)mm | -1/4 | + +------+-------------------------+----+----------------------------------+----------------------+ + .. _BJECIGEB: @@ -845,6 +885,7 @@ a description line containing the following fields: .. _BJEHIBJC: +.. tabularcolumns:: |p{0.1\linewidth}|p{0.5\linewidth}| .. table:: Coil representation accuracies. ======= ===================================================================== diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst index c9a7fee..954912a 100644 --- a/doc/source/manual/matlab.rst +++ b/doc/source/manual/matlab.rst @@ -492,8 +492,8 @@ The documented structures are: ============ =========== ====================================================================== nrow int32 Number of rows. ncol int32 Number of columns. - row_names cell\ The names of associated with the rows. This member may be empty. - col_names cell\ The names of associated with the columns. This member may be empty. + row_names cell(*) The names of associated with the rows. This member may be empty. + col_names cell(*) The names of associated with the columns. This member may be empty. data various The matrix data, usually of type single or double. ============ =========== ====================================================================== @@ -534,8 +534,8 @@ The documented structures are: num_points double Number of integration points. size double Coil size baseline double Coil baseline - description char\ Coil description - coildefs double(num_points,7) Each row contains the integration point weight, followed by location\] and normal + description char(*) Coil description + coildefs double(num_points,7) Each row contains the integration point weight, followed by location [m] and normal FV struct Contains the faces and vertices which can be used to draw the coil for visualization. ============== ======================= ======================================================================================== @@ -551,13 +551,13 @@ The documented structures are: kind int32 The channel type (FIFFV_MEG_CH, FIFF_EEG_CH, etc., see :ref:`BGBJHCGD` ). range double The hardware-oriented part of the calibration factor. This should be only applied to the continuous raw data. cal double The calibration factor to bring the channels to physical units. - loc double(12) The channel location. The first three numbers indicate the location\], followed by the three unit vectors of the channel-specific coordinate frame. These data contain the values saved in the fif file and should not be changed. The values are specified in device coordinates for MEG and in head coordinates for EEG channels, respectively. + loc double(12) The channel location. The first three numbers indicate the location [m], followed by the three unit vectors of the channel-specific coordinate frame. These data contain the values saved in the fif file and should not be changed. The values are specified in device coordinates for MEG and in head coordinates for EEG channels, respectively. coil_trans double(4,4) Initially, transformation from the channel coordinates to device coordinates. This transformation is updated by calls to fiff_transform_meg_chs and fiff_transform_eeg_chs . - eeg_loc double(6) The location of the EEG electrode in coord_frame coordinates. The first three values contain the location of the electrode\]. If six values are present, the remaining ones indicate the location of the reference electrode for this channel. + eeg_loc double(6) The location of the EEG electrode in coord_frame coordinates. The first three values contain the location of the electrode [m]. If six values are present, the remaining ones indicate the location of the reference electrode for this channel. coord_frame int32 Initially, the coordinate frame is FIFFV_COORD_DEVICE for MEG channels and FIFFV_COORD_HEAD for EEG channels. unit int32 Unit of measurement. Relevant values are: 201 = T/m, 112 = T, 107 = V, and 202 = Am. unit_mul int32 The data are given in unit s multiplied by 10unit_mul . Presently, unit_mul is always zero. - ch_name char\ Name of the channel. + ch_name char(*) Name of the channel. coil_def coildef The coil definition structure. This is present only if mne_add_coil_defs has been successfully called. ============== ============== ======================================================================================================================================================================================================================================================================================================================================================= @@ -583,13 +583,14 @@ The documented structures are: ctfkind int32 The kind of the compensation as stored in file. kind int32 ctfkind mapped into small integer numbers. 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. + 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 ================== =============== =========================================================================================================================================================================================================== .. _BGBFHDIJ: +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| .. table:: The meas info structure. ============= ============== ===================================================================================================================== @@ -599,21 +600,22 @@ The documented structures are: meas_id id The ID assigned to this measurement by the acquisition system or during file conversion. nchan int32 Number of channels sfreq double Sampling frequency - highpass double Highpass corner frequency\z]. Zero indicates a DC recording. - lowpass double Lowpass corner frequency\z]. + highpass double Highpass corner frequency [Hz]. Zero indicates a DC recording. + lowpass double Lowpass corner frequency [Hz]. chs ch (nchan) An array of channel information structures. ch_names cell(nchan) Cell array of channel names. dev_head_t trans The device to head transformation ctf_head_t trans The transformation from 4D/CTF head coordinates to Neuromag head coordinates. This is only present in 4D/CTF data. dev_ctf_t trans The transformation from device coordinates to 4D/CTF head coordinates. This is only present in 4D/CTF data - dig dig \ The Polhemus digitization data in head coordinates. - bads cell\ Bad channel list - projs proj \ SSP operator data. - comps comp \ Software gradient compensation data. + dig dig(*) The Polhemus digitization data in head coordinates. + bads cell(*) Bad channel list + projs proj(*) SSP operator data. + comps comp(*) Software gradient compensation data. ============= ============== ===================================================================================================================== .. _BGBEFJCB: +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| .. table:: The surf structure. =============== ================== ============================================================================================================================================================================================================================================================================ @@ -644,6 +646,7 @@ The documented structures are: .. _BGBJJIED: +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| .. table:: The cov structure. ========= ================== ====================================================================================================== @@ -652,10 +655,10 @@ The documented structures are: kind double What kind of a covariance matrix (1 = noise covariance, 2 = source covariance). diag double Is this a diagonal matrix. dim int32 Dimension of the covariance matrix. - names cell\ Names of the channels associated with the entries (may be empty). + names cell(*) Names of the channels associated with the entries (may be empty). data double(dim,dim) The covariance matrix. This a double(dim) vector for a diagonal covariance matrix. - projs proj \ The SSP vectors applied to these data. - bads cell\ Bad channel names. + projs proj(*) The SSP vectors applied to these data. + bads cell(*) Bad channel names. nfree int32 Number of data points used to compute this matrix. eig double(dim) The eigenvalues of the covariance matrix. This field may be empty for a diagonal covariance matrix. eigvec double(dim,dim) The eigenvectors of the covariance matrix. @@ -663,6 +666,7 @@ The documented structures are: .. _BGBFJIBJ: +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| .. table:: The fwd structure. ============== ==================== ============================================================================================================================================================================================================================= @@ -675,13 +679,14 @@ The documented structures are: 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. mri_head_t trans Transformation from the MRI coordinate frame to the (Neuromag) head coordinate frame. - src surf \ The description of the source spaces + src surf(*) The description of the source spaces source_rr double(nsource,3) The source locations. - source_nn double\3) The source orientations. Number of rows is either nsource (fixed source orientations) or 3*nsource (all source orientations). + source_nn double(*,3) The source orientations. Number of rows is either nsource (fixed source orientations) or 3*nsource (all source orientations). ============== ==================== ============================================================================================================================================================================================================================= .. _BGBIEIJE: +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| .. table:: The inv structure. Note: The fields proj , whitener , reginv , and noisenorm are filled in by the routine mne_prepare_inverse_operator. =============== ====================== ============================================================================================================================================================== @@ -692,20 +697,20 @@ The documented structures are: nsource int32 Total number of source space points. nchan int32 Number of channels. coord_frame int32 Coordinate frame in which the locations and orientations are expressed. - source_nn double\3) The source orientations. Number of rows is either nsource (fixed source orientations) or 3*nsource (all source orientations). + source_nn double(*,3) The source orientations. Number of rows is either nsource (fixed source orientations) or 3*nsource (all source orientations). sing double(nchan) The singular values, *i.e.*, the diagonal values of INLINE_EQUATION, see :ref:`CHDBEHBC`. - eigen_leads double\nchan) The matrix INLINE_EQUATION, see :ref:`CHDBEHBC`. + eigen_leads double(*,nchan) The matrix INLINE_EQUATION, see :ref:`CHDBEHBC`. eigen_fields double(nchan,nchan) The matrix INLINE_EQUATION, see :ref:`CHDBEHBC`. noise_cov cov The noise covariance matrix C. source_cov cov The source covariance matrix R. - src surf \ The description of the source spaces + src surf(*) The description of the source spaces mri_head_t trans Transformation from the MRI coordinate frame to the (Neuromag) head coordinate frame. nave double The number of averages. - projs proj \ The SSP vectors which were active when the decomposition was computed + projs proj(*) The SSP vectors which were active when the decomposition was computed proj double(nchan) The projection operator computed using projs . whitener A sparse matrix containing the noise normalization factors. Dimension is either nsource (fixed source orientations) or 3*nsource (all source orientations). reginv double(nchan) The diagonal matrix INLINE_EQUATION, see :ref:`CHDBEHBC`. - noisenorm double\*) A sparse matrix containing the noise normalization factors. Dimension is either nsource (fixed source orientations) or 3*nsource (all source orientations). + noisenorm double(*) A sparse matrix containing the noise normalization factors. Dimension is either nsource (fixed source orientations) or 3*nsource (all source orientations). =============== ====================== ============================================================================================================================================================== On-line documentation for individual routines diff --git a/doc/source/manual/utilities.rst b/doc/source/manual/utilities.rst index a3ca7d0..890453d 100644 --- a/doc/source/manual/utilities.rst +++ b/doc/source/manual/utilities.rst @@ -492,7 +492,7 @@ All lines in the input files starting with the pound sign (#) are considered to be comments. The format of a derivation in a arithmetic input file is: -<name> ``=`` [<INLINE_EQUATION>``*`` ]<INLINE_EQUATION > ``+`` \INLINE_EQUATION>``*`` ]<INLINE_EQUATION >INLINE_EQUATION +<name> ``=`` [<INLINE_EQUATION>``*`` ]<INLINE_EQUATION > ``+`` <INLINE_EQUATION>``*`` ]<INLINE_EQUATION >INLINE_EQUATION where <name> is the name of the derived channel, INLINE_EQUATION are @@ -1266,9 +1266,9 @@ The available variables are listed in :ref:`CHDJBIEE`. ================ ======================================= Variable Meaning ================ ======================================= - x time\] - t current value of x in\s] - y the source amplitude\m] + x time [s] + t current value of x in [ms] + y the source amplitude [Am] q synonym for y a , b , c , d help variables, initialized to zeros ================ ======================================= -- 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
