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commit 240886c2cd5ec2e54078d088e9aadee0d932dc84 Author: Alexandre Gramfort <[email protected]> Date: Fri Jul 8 13:10:14 2011 +0200 DOC: better latex doc --- doc/source/manual/convert.rst | 415 ++++++++++++++++++++++++++++------------ doc/source/manual/matlab.rst | 38 ++-- doc/source/manual/utilities.rst | 124 ++++++++---- 3 files changed, 396 insertions(+), 181 deletions(-) diff --git a/doc/source/manual/convert.rst b/doc/source/manual/convert.rst index 3e1bc44..71ddef2 100755 --- a/doc/source/manual/convert.rst +++ b/doc/source/manual/convert.rst @@ -1669,54 +1669,55 @@ Guide to combining options The combination of options is quite complicated. The :ref:`BEHDCIII` should be helpful to determine the combination of options appropriate for your needs. -.. _BEHDCIII: +.. tabularcolumns:: |p{0.38\linewidth}|p{0.1\linewidth}|p{0.2\linewidth}|p{0.3\linewidth}| +.. _BEHDCIII: .. table:: Guide to combining mne_convert_mne_data options. +-------------------------------------+---------+--------------------------+-----------------------+ | Desired output | Format | Required options | Optional options | +-------------------------------------+---------+--------------------------+-----------------------+ - | forward model | fif | | \---fwd <*name*> | \---bad <*name*> | - | | | | \---out <*name*> | \---surfsrc | - | | | | \---meg and/or \---eeg | | - | | | | \---fif | | + | forward model | fif | \---fwd <*name*> | \---bad <*name*> | + | | | \---out <*name*> | \---surfsrc | + | | | \---meg and/or \---eeg | | + | | | \---fif | | +-------------------------------------+---------+--------------------------+-----------------------+ - | forward model | mat | | \---fwd <*name*> | \---bad <*name*> | - | | | | \---out <*name*> | \---surfsrc | - | | | | \---meg and/or --eeg | | + | forward model | mat | \---fwd <*name*> | \---bad <*name*> | + | | | \---out <*name*> | \---surfsrc | + | | | \---meg and/or --eeg | | +-------------------------------------+---------+--------------------------+-----------------------+ - | forward model and sensor covariance | mat | | \---fwd <*name*> | \---bad <*name*> | - | | | | \---out <*name*> | \---surfsrc | - | | | | \---senscov <*name*> | | - | | | | \---meg and/or --eeg | | + | forward model and sensor covariance | mat | \---fwd <*name*> | \---bad <*name*> | + | | | \---out <*name*> | \---surfsrc | + | | | \---senscov <*name*> | | + | | | \---meg and/or --eeg | | +-------------------------------------+---------+--------------------------+-----------------------+ - | sensor covariance | fif | | \---fwd <*name*> | \---bad <*name*> | - | | | | \---out <*name*> | | - | | | | \---senscov <*name*> | | - | | | | \---noiseonly | | - | | | | \---fif | | - | | | | \---meg and/or --eeg | | + | sensor covariance | fif | \---fwd <*name*> | \---bad <*name*> | + | | | \---out <*name*> | | + | | | \---senscov <*name*> | | + | | | \---noiseonly | | + | | | \---fif | | + | | | \---meg and/or --eeg | | +-------------------------------------+---------+--------------------------+-----------------------+ - | sensor covariance | mat | | \---senscov <*name*> | \---bad <*name*> | - | | | | \---out <*name*> | | + | sensor covariance | mat | \---senscov <*name*> | \---bad <*name*> | + | | | \---out <*name*> | | +-------------------------------------+---------+--------------------------+-----------------------+ - | sensor covariance eigenvalues | text | | \---senscov <*name*> | \---bad <*name*> | - | | | | \---out <*name*> | | - | | | | \---eig | | + | sensor covariance eigenvalues | text | \---senscov <*name*> | \---bad <*name*> | + | | | \---out <*name*> | | + | | | \---eig | | +-------------------------------------+---------+--------------------------+-----------------------+ - | evoked MEG/EEG data | mat | | \---meas <*name*> | \---sel <*name*> | - | | | | \---out <*name*> | \---set <*number*> | + | evoked MEG/EEG data | mat | \---meas <*name*> | \---sel <*name*> | + | | | \---out <*name*> | \---set <*number*> | +-------------------------------------+---------+--------------------------+-----------------------+ - | evoked MEG/EEG data forward model | mat | | \---meas <*name*> | \---bad <*name*> | - | | | | \---fwd <*name*> | \---set <*number*> | - | | | | \---out <*name*> | | + | evoked MEG/EEG data forward model | mat | \---meas <*name*> | \---bad <*name*> | + | | | \---fwd <*name*> | \---set <*number*> | + | | | \---out <*name*> | | +-------------------------------------+---------+--------------------------+-----------------------+ - | inverse operator data | mat | | \---inv <*name*> | | - | | | | \---out <*name*> | | + | inverse operator data | mat | \---inv <*name*> | | + | | | \---out <*name*> | | +-------------------------------------+---------+--------------------------+-----------------------+ - | inverse operator data evoked | mat | | \–--inv <*name*> | | - | MEG/EEG data | | | \–--meas <*name*> | | - | | | | \–--out <*name*> | | + | inverse operator data evoked | mat | \–--inv <*name*> | | + | MEG/EEG data | | \–--meas <*name*> | | + | | | \–--out <*name*> | | +-------------------------------------+---------+--------------------------+-----------------------+ Matlab data structures @@ -1750,7 +1751,6 @@ The symbols employed in variable size descriptions are: of time points in the measurement data. .. _BEHCICCA: - .. table:: Matlab structures produced by mne_convert_mne_data. =============== ======================================= @@ -1764,41 +1764,110 @@ The symbols employed in variable size descriptions are: The prefix given with the ``--tag`` option is indicated <*tag*> , see :ref:`BEHCICCF`. Its default value is MNE. -.. _BABCBIGF: +.. tabularcolumns:: |p{0.14\linewidth}|p{0.13\linewidth}|p{0.73\linewidth}| +.. _BABCBIGF: .. table:: The fields of Matlab structures. - =================== ================== =============================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...] - Variable Size Description - =================== ================== =============================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...] - fwd nsource x nchan The forward solution, one source on each row. For free orientation sources, the fields of the three orthogonal dipoles for each location are listed consecutively. - names ch_names nchan (string) String array containing the names of the channels included - ch_types nchan x 2 The column lists the types of the channels (1 = MEG, 2 = EEG). The second column lists the coil types, see Tables 5.2 and 5.3. For EEG electrodes, this value equals one. - ch_pos nchan x 3 The location information for each channel. The first three values specify the origin of the sensor coordinate system or the location of the electrode. For MEG channels, the following nine number specify the *x*, *y*, and *z*-direction unit vectors of the sensor coordinate system. For EEG electrodes the first unit vector specifies the location of the reference electrode. If the reference is not specified this value is all zeroes. The remaining [...] - ch_lognos nchan x 1 Logical channel numbers as listed in the fiff file - ch_units nchan x 2 Units and unit multipliers as listed in the fif file. The unit of the data is listed in the first column (T = 112, T/m = 201, V = 107). At present, the second column will be always zero, *i.e.*, no unit multiplier. - ch_cals nchan x 2 Even if the data comes from the conversion already calibrated, the original calibration factors are included. The first column is the range member of the fif data structures and while the second is the cal member. To get calibrated values in the units given in ch_units from the raw data, the data must be multiplied with the product of range and cal . - sfreq 1 The sampling frequency in Hz. - lowpass 1 Lowpass filter frequency (Hz) - highpass 1 Highpass filter frequency (Hz) - source_loc nloc x 3 The source locations given in the coordinate frame indicated by the coord_frame member. - source_ori nsource x 3 The source orientations - source_selection nsource x 2 Indication of the sources selected from the complete source spaces. Each row contains the number of the source in the complete source space (starting with 0) and the source space number (1 or 2). These numbers refer to the order the two hemispheres where listed when mne_make_source_space was invoked. mne_setup_source_space lists the left hemisphere first. - coord_frame string Name of the coordinate frame employed in the forward calculations. Possible values are 'head' and 'mri'. - mri_head_trans 4 x 4 The coordinate frame transformation from mri the MEG 'head' coordinates. - meg_head_trans 4 x 4 The coordinate frame transformation from the MEG device coordinates to the MEG head coordinates - noise_cov nchan x nchan The noise covariance matrix - source_cov nsource The elements of the diagonal source covariance matrix. - sing nchan The singular values of :math:`A = C_0^{-^1/_2} G R^C = U \Lambda V^T` with :math:`R` selected so that :math:`\text{trace}(AA^T) / \text{trace}(I) = 1` as discussed in :ref:`CHDDHAGE` - eigen_fields nchan x nchan The rows of this matrix are the left singular vectors of :math:`A`, i.e., the columns of :math:`U`, see above. - eigen_leads nchan x nsource The rows of this matrix are the right singular vectors of :math:`A`, i.e., the columns of :math:`V`, see above. - noise_eigenval nchan In terms of :ref:`CHDDHAGE`, eigenvalues of :math:`C_0`, i.e., not scaled with number of averages. - noise_eigenvec nchan Eigenvectors of the noise covariance matrix. In terms of :ref:`CHDDHAGE`, :math:`U_C^T`. - data nchan x ntime The measured data. One row contains the data at one time point. - times ntime The time points in the above matrix in seconds - nave 1 Number of averages as listed in the data file. - meas_times ntime The time points in seconds. - =================== ================== =============================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...] + + +-----------------------+-----------------+------------------------------------------------------------+ + | Variable | Size | Description | + +-----------------------+-----------------+------------------------------------------------------------+ + | fwd | nsource x nchan | The forward solution, one source on each row. For free | + | | | orientation sources, the fields of the three orthogonal | + | | | dipoles for each location are listed consecutively. | + +-----------------------+-----------------+------------------------------------------------------------+ + | names ch_names | nchan (string) | String array containing the names of the channels included | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_types | nchan x 2 | The column lists the types of the channels (1 = MEG, | + | | | 2 = EEG). The second column lists the coil types, see | + | | | :ref:`BGBBHGEC` and :ref:`CHDBDFJE`. For EEG electrodes, | + | | | this value equals one. | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_pos | nchan x 3 | The location information for each channel. The first three | + | | | values specify the origin of the sensor coordinate system | + | | | or the location of the electrode. For MEG channels, the | + | | | following nine number specify the *x*, *y*, and | + | | | *z*-direction unit vectors of the sensor coordinate system.| + | | | For EEG electrodes the first unit vector specifies the | + | | | location of the reference electrode. If the reference is | + | | | not specified this value is all zeroes. The remaining unit | + | | | vectors are irrelevant for EEG electrodes. | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_lognos | nchan x 1 | Logical channel numbers as listed in the fiff file | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_units | nchan x 2 | Units and unit multipliers as listed in the fif file. The | + | | | unit of the data is listed in the first column (T = 112, | + | | | T/m = 201, V = 107). At present, the second column will be | + | | | always zero, *i.e.*, no unit multiplier. | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_cals | nchan x 2 | Even if the data comes from the conversion already | + | | | calibrated, the original calibration factors are included. | + | | | The first column is the range member of the fif data | + | | | structures and while the second is the cal member. To get | + | | | calibrated values in the units given in ch_units from the | + | | | raw data, the data must be multiplied with the product of | + | | | range and cal. | + +-----------------------+-----------------+------------------------------------------------------------+ + | sfreq | 1 | The sampling frequency in Hz. | + +-----------------------+-----------------+------------------------------------------------------------+ + | lowpass | 1 | Lowpass filter frequency (Hz) | + +-----------------------+-----------------+------------------------------------------------------------+ + | highpass | 1 | Highpass filter frequency (Hz) | + +-----------------------+-----------------+------------------------------------------------------------+ + | source_loc | nloc x 3 | The source locations given in the coordinate frame | + | | | indicated by the coord_frame member. | + +-----------------------+-----------------+------------------------------------------------------------+ + | source_ori | nsource x 3 | The source orientations | + +-----------------------+-----------------+------------------------------------------------------------+ + | source_selection | nsource x 2 | Indication of the sources selected from the complete source| + | | | spaces. Each row contains the number of the source in the | + | | | complete source space (starting with 0) and the source | + | | | space number (1 or 2). These numbers refer to the order the| + | | | two hemispheres where listed when mne_make_source_space was| + | | | invoked. mne_setup_source_space lists the left hemisphere | + | | | first. | + +-----------------------+-----------------+------------------------------------------------------------+ + | coord_frame | string | Name of the coordinate frame employed in the forward | + | | | calculations. Possible values are 'head' and 'mri'. | + +-----------------------+-----------------+------------------------------------------------------------+ + | mri_head_trans | 4 x 4 | The coordinate frame transformation from mri the MEG 'head'| + | | | coordinates. | + +-----------------------+-----------------+------------------------------------------------------------+ + | meg_head_trans | 4 x 4 | The coordinate frame transformation from the MEG device | + | | | coordinates to the MEG head coordinates | + +-----------------------+-----------------+------------------------------------------------------------+ + | noise_cov | nchan x nchan | The noise covariance matrix | + +-----------------------+-----------------+------------------------------------------------------------+ + | source_cov | nsource | The elements of the diagonal source covariance matrix. | + +-----------------------+-----------------+------------------------------------------------------------+ + | sing | nchan | The singular values of | + | | | :math:`A = C_0^{-^1/_2} G R^C = U \Lambda V^T` | + | | | with :math:`R` selected so that | + | | | :math:`\text{trace}(AA^T) / \text{trace}(I) = 1` | + | | | as discussed in :ref:`CHDDHAGE` | + +-----------------------+-----------------+------------------------------------------------------------+ + | eigen_fields | nchan x nchan | The rows of this matrix are the left singular vectors of | + | | | :math:`A`, i.e., the columns of :math:`U`, see above. | + +-----------------------+-----------------+------------------------------------------------------------+ + | eigen_leads | nchan x nsource | The rows of this matrix are the right singular vectors of | + | | | :math:`A`, i.e., the columns of :math:`V`, see above. | + +-----------------------+-----------------+------------------------------------------------------------+ + | noise_eigenval | nchan | In terms of :ref:`CHDDHAGE`, eigenvalues of :math:`C_0`, | + | | | i.e., not scaled with number of averages. | + +-----------------------+-----------------+------------------------------------------------------------+ + | noise_eigenvec | nchan | Eigenvectors of the noise covariance matrix. In terms of | + | | | :ref:`CHDDHAGE`, :math:`U_C^T`. | + +-----------------------+-----------------+------------------------------------------------------------+ + | data | nchan x ntime | The measured data. One row contains the data at one time | + | | | point. | + +-----------------------+-----------------+------------------------------------------------------------+ + | times | ntime | The time points in the above matrix in seconds | + +-----------------------+-----------------+------------------------------------------------------------+ + | nave | 1 | Number of averages as listed in the data file. | + +-----------------------+-----------------+------------------------------------------------------------+ + | meas_times | ntime | The time points in seconds. | + +-----------------------+-----------------+------------------------------------------------------------+ .. _convert_to_matlab: @@ -1870,41 +1939,87 @@ The fields of the <*tag*>_raw_info structure are listed in :ref:`BEHFDCIH`. Further explanation of the bufs field is provided in :ref:`BEHJEIHJ`. -.. _BEHFDCIH: +.. tabularcolumns:: |p{0.2\linewidth}|p{0.15\linewidth}|p{0.6\linewidth}| +.. _BEHFDCIH: .. table:: The fields of the raw data info structure. - ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...] - Variable Size Description - ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...] - orig_file string The name of the original fif file specified with the ``--raw`` option. - nchan 1 Number of channels. - nsamp 1 Total number of samples - bufs nbuf x 4 This field is present if ``--info`` option was specified on the command line. For details, see :ref:`BEHJEIHJ`. - sfreq 1 The sampling frequency in Hz. - lowpass 1 Lowpass filter frequency (Hz) - highpass 1 Highpass filter frequency (Hz) - ch_names nchan (string) String array containing the names of the channels included - ch_types nchan x 2 The column lists the types of the channesl (1 = MEG, 2 = EEG). The second column lists the coil types, see Tables 5.2 and 5.3. For EEG electrodes, this value equals one. - ch_lognos nchan x 1 Logical channel numbers as listed in the fiff file - ch_units nchan x 2 Units and unit multipliers as listed in the fif file. The unit of the data is listed in the first column (T = 112, T/m = 201, V = 107). At present, the second column will be always zero, *i.e.*, no unit multiplier. - ch_pos nchan x 12 The location information for each channel. The first three values specify the origin of the sensor coordinate system or the location of the electrode. For MEG channels, the following nine number specify the *x*, *y*, and *z*-direction unit vectors of the sensor coordinate system. For EEG electrodes the first vector after the electrode location specifies the location of the reference electrode. If the reference is not specified this value is all z [...] - ch_cals nchan x 2 The raw data output by mne_raw2mat is uncalibrated. The first column is the range member of the fiff data structures and while the second is the cal member. To get calibrared data values in the units given in ch_units from the raw data, the data must be multiplied with the product of range and cal . - meg_head_trans 4 x 4 The coordinate frame transformation from the MEG device coordinates to the MEG head coordinates. - ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...] - + +-----------------------+-----------------+------------------------------------------------------------+ + | Variable | Size | Description | + +-----------------------+-----------------+------------------------------------------------------------+ + | orig_file | string | The name of the original fif file specified with the | + | | | ``--raw`` option. | + +-----------------------+-----------------+------------------------------------------------------------+ + | nchan | 1 | Number of channels. | + +-----------------------+-----------------+------------------------------------------------------------+ + | nsamp | 1 | Total number of samples | + +-----------------------+-----------------+------------------------------------------------------------+ + | bufs | nbuf x 4 | This field is present if ``--info`` option was specified on| + | | | the command line. For details, see :ref:`BEHJEIHJ`. | + +-----------------------+-----------------+------------------------------------------------------------+ + | sfreq | 1 | The sampling frequency in Hz. | + +-----------------------+-----------------+------------------------------------------------------------+ + | lowpass | 1 | Lowpass filter frequency (Hz) | + +-----------------------+-----------------+------------------------------------------------------------+ + | highpass | 1 | Highpass filter frequency (Hz) | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_names | nchan (string) | String array containing the names of the channels included | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_types | nchan x 2 | The column lists the types of the channesl (1 = MEG, 2 = | + | | | EEG). The second column lists the coil types, see | + | | | :ref:`BGBBHGEC` and :ref:`CHDBDFJE`. For EEG electrodes, | + | | | this value equals one. | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_lognos | nchan x 1 | Logical channel numbers as listed in the fiff file | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_units | nchan x 2 | Units and unit multipliers as listed in the fif file. | + | | | The unit of the data is listed in the first column | + | | | (T = 112, T/m = 201, V = 107). At present, the second | + | | | column will be always zero, *i.e.*, no unit multiplier. | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_pos | nchan x 12 | The location information for each channel. The first three | + | | | values specify the origin of the sensor coordinate system | + | | | or the location of the electrode. For MEG channels, the | + | | | following nine number specify the *x*, *y*, and | + | | | *z*-direction unit vectors of the sensor coordinate system.| + | | | For EEG electrodes the first vector after the electrode | + | | | location specifies the location of the reference electrode.| + | | | If the reference is not specified this value is all zeroes.| + | | | The remaining unit vectors are irrelevant for EEG | + | | | electrodes. | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_cals | nchan x 2 | The raw data output by mne_raw2mat is uncalibrated. | + | | | The first column is the range member of the fiff data | + | | | structures and while the second is the cal member. To get | + | | | calibrared data values in the units given in ch_units from | + | | | the raw data, the data must be multiplied with the product | + | | | of range and cal . | + +-----------------------+-----------------+------------------------------------------------------------+ + | meg_head_trans | 4 x 4 | The coordinate frame transformation from the MEG device | + | | | coordinates to the MEG head coordinates. | + +-----------------------+-----------------+------------------------------------------------------------+ + + +.. tabularcolumns:: |p{0.1\linewidth}|p{0.6\linewidth}| .. _BEHJEIHJ: - .. table:: The bufs member of the raw data info structure. - ======== =========================================================================================================================================================================================================================== - Column Contents - ======== =========================================================================================================================================================================================================================== - 1 The raw data type (2 or 16 = 2-byte signed integer, 3 = 4-byte signed integer, 4 = single-precision float). All data in the fif file are written in the big-endian byte order. The raw data are stored sample by sample. - 2 Byte location of this buffer in the original fif file. - 3 First sample of this buffer. Since raw data storing can be switched on and off during the acquisition, there might be gaps between the end of one buffer and the beginning of the next. - 4 Number of samples in the buffer. - ======== =========================================================================================================================================================================================================================== + +-----------------------+-------------------------------------------------------------------------+ + | Column | Contents | + +-----------------------+-------------------------------------------------------------------------+ + | 1 | The raw data type (2 or 16 = 2-byte signed integer, 3 = 4-byte signed | + | | integer, 4 = single-precision float). All data in the fif file are | + | | written in the big-endian byte order. The raw data are stored sample by | + | | sample. | + +-----------------------+-------------------------------------------------------------------------+ + | 2 | Byte location of this buffer in the original fif file. | + +-----------------------+-------------------------------------------------------------------------+ + | 3 | First sample of this buffer. Since raw data storing can be switched on | + | | and off during the acquisition, there might be gaps between the end of | + | | one buffer and the beginning of the next. | + +-----------------------+-------------------------------------------------------------------------+ + | 4 | Number of samples in the buffer. | + +-----------------------+-------------------------------------------------------------------------+ .. _BEHFIDCB: @@ -2087,7 +2202,7 @@ The data are not calibrated, i.e., the calibration factors present in the Matlab description file have to be applied to get to physical units as described below. -.. note:: The maximum size of an epoch data file is 2 Gbytes, *i.e.*, 0.5 Gsamples. +.. note:: The maximum size of an epoch data file is 2 Gbytes, *i.e.*, 0.5 Gsamples. Matlab data structures ====================== @@ -2098,42 +2213,88 @@ The fields of the this structure are listed in :ref:`BEHFDCIH`. Further explanation of the epochs member is provided in :ref:`BEHHAGHE`. -.. _BEHIFJIJ: +.. tabularcolumns:: |p{0.15\linewidth}|p{0.15\linewidth}|p{0.6\linewidth}| +.. _BEHIFJIJ: .. table:: The fields of the raw data info structure. - ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...] - Variable Size Description - ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...] - orig_file string The name of the original fif file specified with the ``--raw`` option. - epoch_file string The name of the epoch data file produced by mne_epocs2mat . - nchan 1 Number of channels. - nepoch 1 Total number of epochs. - epochs nepoch x 5 Description of the content of the epoch data file, see :ref:`BEHHAGHE`. - sfreq 1 The sampling frequency in Hz. - lowpass 1 Lowpass filter frequency (Hz) - highpass 1 Highpass filter frequency (Hz) - ch_names nchan (string) String array containing the names of the channels included - ch_types nchan x 2 The column lists the types of the channels (1 = MEG, 2 = EEG). The second column lists the coil types, see Tables 5.2 and 5.3. For EEG electrodes, this value equals one. - ch_lognos nchan x 1 Logical channel numbers as listed in the fiff file - ch_units nchan x 2 Units and unit multipliers as listed in the fif file. The unit of the data is listed in the first column (T = 112, T/m = 201, V = 107). At present, the second column will be always zero, *i.e.*, no unit multiplier. - ch_pos nchan x 12 The location information for each channel. The first three values specify the origin of the sensor coordinate system or the location of the electrode. For MEG channels, the following nine number specify the *x*, *y*, and *z*-direction unit vectors of the sensor coordinate system. For EEG electrodes the first vector after the electrode location specifies the location of the reference electrode. If the reference is not specified this value is all z [...] - ch_cals nchan x 2 The raw data output by mne_raw2mat are not calibrated. The first column is the range member of the fiff data structures and while the second is the cal member. To get calibrated data values in the units given in ch_units from the raw data, the data must be multiplied with the product of range and cal . - meg_head_trans 4 x 4 The coordinate frame transformation from the MEG device coordinates to the MEG head coordinates. - ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...] - + +-----------------------+-----------------+------------------------------------------------------------+ + | Variable | Size | Description | + +-----------------------+-----------------+------------------------------------------------------------+ + | orig_file | string | The name of the original fif file specified with the | + | | | ``--raw`` option. | + +-----------------------+-----------------+------------------------------------------------------------+ + | epoch_file | string | The name of the epoch data file produced by mne_epocs2mat. | + +-----------------------+-----------------+------------------------------------------------------------+ + | nchan | 1 | Number of channels. | + +-----------------------+-----------------+------------------------------------------------------------+ + | nepoch | 1 | Total number of epochs. | + +-----------------------+-----------------+------------------------------------------------------------+ + | epochs | nepoch x 5 | Description of the content of the epoch data file, | + | | | see :ref:`BEHHAGHE`. | + +-----------------------+-----------------+------------------------------------------------------------+ + | sfreq | 1 | The sampling frequency in Hz. | + +-----------------------+-----------------+------------------------------------------------------------+ + | lowpass | 1 | Lowpass filter frequency (Hz) | + +-----------------------+-----------------+------------------------------------------------------------+ + | highpass | 1 | Highpass filter frequency (Hz) | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_names | nchan (string) | String array containing the names of the channels included | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_types | nchan x 2 | The column lists the types of the channels (1 = MEG, 2 = | + | | | EEG). The second column lists the coil types, see | + | | | :ref:`BGBBHGEC` and :ref:`CHDBDFJE`. For EEG electrodes, | + | | | this value equals one. | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_lognos | nchan x 1 | Logical channel numbers as listed in the fiff file | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_units | nchan x 2 | Units and unit multipliers as listed in the fif file. | + | | | The unit of the data is listed in the first column | + | | | (T = 112, T/m = 201, V = 107). At present, the second | + | | | column will be always zero, *i.e.*, no unit multiplier. | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_pos | nchan x 12 | The location information for each channel. The first three | + | | | values specify the origin of the sensor coordinate system | + | | | or the location of the electrode. For MEG channels, the | + | | | following nine number specify the *x*, *y*, and | + | | | *z*-direction unit vectors of the sensor coordinate | + | | | system. For EEG electrodes the first vector after the | + | | | electrode location specifies the location of the reference | + | | | electrode. If the reference is not specified this value is | + | | | all zeroes. The remaining unit vectors are irrelevant for | + | | | EEG electrodes. | + +-----------------------+-----------------+------------------------------------------------------------+ + | ch_cals | nchan x 2 | The raw data output by mne_raw2mat are not calibrated. | + | | | The first column is the range member of the fiff data | + | | | structures and while the second is the cal member. To | + | | | get calibrated data values in the units given in | + | | | ch_units from the raw data, the data must be multiplied | + | | | with the product of range and cal . | + +-----------------------+-----------------+------------------------------------------------------------+ + | meg_head_trans | 4 x 4 | The coordinate frame transformation from the MEG device | + | | | coordinates to the MEG head coordinates. | + +-----------------------+-----------------+------------------------------------------------------------+ + + +.. tabularcolumns:: |p{0.2\linewidth}|p{0.6\linewidth}| .. _BEHHAGHE: - .. table:: The epochs member of the raw data info structure. - ======== ================================================================================================================================================================================================================ - Column Contents - ======== ================================================================================================================================================================================================================ - 1 The raw data type (2 or 16 = 2-byte signed integer, 3 = 4-byte signed integer, 4 = single-precision float). The epoch data are written using the big-endian byte order. The data are stored sample by sample. - 2 Byte location of this epoch in the binary epoch file. - 3 First sample of this epoch in the original raw data file. - 4 First sample of the epoch with respect to the event. - 5 Number of samples in the epoch. - ======== ================================================================================================================================================================================================================ + +---------------+------------------------------------------------------------------+ + | Column | Contents | + +---------------+------------------------------------------------------------------+ + | 1 | The raw data type (2 or 16 = 2-byte signed integer, 3 = 4-byte | + | | signed integer, 4 = single-precision float). The epoch data are | + | | written using the big-endian byte order. The data are stored | + | | sample by sample. | + +---------------+------------------------------------------------------------------+ + | 2 | Byte location of this epoch in the binary epoch file. | + +---------------+------------------------------------------------------------------+ + | 3 | First sample of this epoch in the original raw data file. | + +---------------+------------------------------------------------------------------+ + | 4 | First sample of the epoch with respect to the event. | + +---------------+------------------------------------------------------------------+ + | 5 | Number of samples in the epoch. | + +---------------+------------------------------------------------------------------+ .. note:: For source modelling purposes, it is recommended that the MNE Matlab toolbox, see :ref:`ch_matlab` is employed to read the measurement info instead of using the channel information in the raw data info structure described in :ref:`BEHIFJIJ`. diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst index 044a323..6c4fb19 100755 --- a/doc/source/manual/matlab.rst +++ b/doc/source/manual/matlab.rst @@ -36,6 +36,7 @@ they are listed in :ref:`BGBEFADJ`. .. note:: The matlab function fiff_setup_read_raw has a significant change. The sample numbers now take into account possible initial skip in the file, *i.e.*, the time between the start of the data acquisition and the start of saving the data to disk. The first_samp member of the returned structure indicates the initial skip in samples. If you want your own routines, which assume that initial skip has been removed, perform identically with the previous version, subt [...] +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. _BGBCGHAG: .. table:: High-level reading routines. @@ -69,6 +70,7 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. table:: Channel selection utilities. +--------------------------------+--------------------------------------------------------------+ @@ -92,6 +94,7 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. table:: Coordinate transformation utilities. +--------------------------------+--------------------------------------------------------------+ @@ -110,6 +113,7 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. table:: Basic reading routines. +--------------------------------+--------------------------------------------------------------+ @@ -137,6 +141,7 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. table:: Writing routines. +--------------------------------+--------------------------------------------------------------+ @@ -194,6 +199,7 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. table:: High-level data writing routines. +--------------------------------+--------------------------------------------------------------+ @@ -213,6 +219,7 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. table:: Coil definition utilities. +--------------------------------+--------------------------------------------------------------+ @@ -224,7 +231,7 @@ they are listed in :ref:`BGBEFADJ`. | mne_load_coil_def | Load a coil definition file. | +--------------------------------+--------------------------------------------------------------+ - +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. table:: Routines for software gradient compensation and signal-space projection. +--------------------------------+--------------------------------------------------------------+ @@ -251,6 +258,7 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. table:: High-level routines for reading MNE data files. +--------------------------------+--------------------------------------------------------------+ @@ -283,6 +291,7 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. table:: High-level routines for writing MNE data files. +--------------------------------+--------------------------------------------------------------+ @@ -303,8 +312,8 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. _BABBDDAI: - .. table:: Routines related to stc, w, and label files. +--------------------------------+--------------------------------------------------------------+ @@ -347,6 +356,7 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. table:: Routines for reading FreeSurfer surfaces. +--------------------------------+--------------------------------------------------------------+ @@ -368,8 +378,8 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. _BGBEGFBD: - .. table:: Utility functions. +--------------------------------+--------------------------------------------------------------+ @@ -412,8 +422,8 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ +.. tabularcolumns:: |p{0.3\linewidth}|p{0.6\linewidth}| .. _BGBEFADJ: - .. table:: Examples demonstrating the use of the toolbox. +--------------------------------+--------------------------------------------------------------+ @@ -531,13 +541,14 @@ The documented structures are: .. note:: The MNE Matlab toolbox tries it best to employ vertex numbering starting from 1 as opposed to 0 as recorded in the data files. There are, however, two exceptions where explicit attention to the vertex numbering convention is needed. First, the standard stc and w file reading and writing routines return and assume zero-based vertex numbering. There are now versions with names ending with '1', which return and assume one-based vertex numbering, see :ref:`BABBDDAI`. Second, the [...] -.. _BGBJHCGD: +.. tabularcolumns:: |p{0.38\linewidth}|p{0.06\linewidth}|p{0.46\linewidth}| +.. _BGBJHCGD: .. table:: FIFF constants. +-------------------------------+-------+----------------------------------------------------------+ | Name | Value | Purpose | - +===============================+=======+==========================================================+ + +-------------------------------+-------+----------------------------------------------------------+ | FIFFV_MEG_CH | 1 | This is a MEG channel. | +-------------------------------+-------+----------------------------------------------------------+ | FIFFV_REF_MEG_CH | 301 | This a reference MEG channel, located far away from the | @@ -755,8 +766,9 @@ The documented structures are: data various The matrix data, usually of type single or double. ============ =========== ====================================================================== -.. _BGBDHBIF: +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| +.. _BGBDHBIF: .. table:: The trans structure. +---------------------------+-----------+----------------------------------------------------------+ @@ -773,8 +785,8 @@ The documented structures are: +---------------------------+-----------+----------------------------------------------------------+ +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| .. _BGBHDEDG: - .. table:: The dig structure. +---------------------------+-----------+----------------------------------------------------------+ @@ -790,8 +802,8 @@ The documented structures are: +---------------------------+-----------+----------------------------------------------------------+ +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| .. _BGBGBEBH: - .. table:: The coildef structure. For more detailed information, see :ref:`BJEIAEIE`. +-------------------+-------------------+----------------------------------------------------------+ @@ -819,8 +831,8 @@ The documented structures are: +-------------------+-------------------+----------------------------------------------------------+ +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| .. _BGBIABGD: - .. table:: The ch structure. +---------------------------+-----------+----------------------------------------------------------+ @@ -875,8 +887,8 @@ The documented structures are: +---------------------------+-----------+----------------------------------------------------------+ +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| .. _BGBCJHJB: - .. table:: The proj structure. +---------------------------+-----------+----------------------------------------------------------+ @@ -895,8 +907,9 @@ The documented structures are: +---------------------------+-----------+----------------------------------------------------------+ -.. _BGBJDIFD: +.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| +.. _BGBJDIFD: .. table:: The comp structure. +---------------------------+-----------+----------------------------------------------------------+ @@ -926,7 +939,6 @@ The documented structures are: .. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}| .. _BGBFHDIJ: - .. table:: The meas info structure. +---------------------------+-----------+----------------------------------------------------------+ diff --git a/doc/source/manual/utilities.rst b/doc/source/manual/utilities.rst index a76383c..82a6ba1 100755 --- a/doc/source/manual/utilities.rst +++ b/doc/source/manual/utilities.rst @@ -1281,52 +1281,94 @@ expressions. .. _CHDJIBHA: +.. tabularcolumns:: |p{0.2\linewidth}|p{0.6\linewidth}| .. table:: Mathematical functions available for source waveform expressions - ================ =============================================================================================================================================================================================================================== - Function Description - ================ =============================================================================================================================================================================================================================== - abs(x) absolute value - acos(x) :math:`\cos^{-1}x` - asin(x) :math:`\sin^{-1}x` - atan(x) :math:`\tan^{-1}x` - atan2(x,y) :math:`\tan^{-1}(^y/_x)` - ceil(x) nearest integer larger than :math:`x` - cos(x) :math:`\cos x` - cosw(x,a,b,c) :math:`\cos^2` -shaped window centered at :math:`b` with a rising slope of length :math:`a` and a trailing slope of length :math:`b`. - deg(x) The value of :math:`x` converted to from radians to degrees - erf(x) :math:`\frac{1}{2\pi} \int_0^x{\text{exp}(-t^2)dt}` - erfc(x) :math:`1 - \text{erf}(x)` - exp(x) :math:`e^x` - floor(x) Largest integer value not larger than :math:`x` - hypot(x,y) :math:`\sqrt{x^2 + y^2}` - ln(x) :math:`\ln x` - log(x) :math:`\log_{10} x` - maxp(x,y) Takes the maximum between :math:`x` and :math:`y` - minp(x,y) Takes the minimum between :math:`x` and :math:`y` - mod(x,y) Gives the remainder of :math:`x` divided by :math:`y` - pi Ratio of the circumference of a circle and its diameter. - rand Gives a vector of uniformly distributed random numbers from 0 to 1. - rnorm(x,y) Gives a vector of Gaussian random numbers distributed as :math:`N(x,y)`. Note that if :math:`x` and :math:`y` are vectors, each number generated will a different mean and variance according to the arguments. - shift(x,s) Shifts the values in the input vector :math:`x` by the number of positions given by :math:`s`. Note that :math:`s` must be a scalar. - sin(x) :math:`\sin x` - sqr(x) :math:`x^2` - sqrt(x) :math:`\sqrt{x}` - tan(x) :math:`\tan x` - ================ =============================================================================================================================================================================================================================== - + +-----------------------+---------------------------------------------------------------+ + | Function | Description | + +-----------------------+---------------------------------------------------------------+ + | abs(x) | absolute value | + +-----------------------+---------------------------------------------------------------+ + | acos(x) | :math:`\cos^{-1}x` | + +-----------------------+---------------------------------------------------------------+ + | asin(x) | :math:`\sin^{-1}x` | + +-----------------------+---------------------------------------------------------------+ + | atan(x) | :math:`\tan^{-1}x` | + +-----------------------+---------------------------------------------------------------+ + | atan2(x,y) | :math:`\tan^{-1}(^y/_x)` | + +-----------------------+---------------------------------------------------------------+ + | ceil(x) | nearest integer larger than :math:`x` | + +-----------------------+---------------------------------------------------------------+ + | cos(x) | :math:`\cos x` | + +-----------------------+---------------------------------------------------------------+ + | cosw(x,a,b,c) | :math:`\cos^2` -shaped window centered at :math:`b` with a | + | | rising slope of length :math:`a` and a trailing slope of | + | | length :math:`b`. | + +-----------------------+---------------------------------------------------------------+ + | deg(x) | The value of :math:`x` converted to from radians to degrees | + +-----------------------+---------------------------------------------------------------+ + | erf(x) | :math:`\frac{1}{2\pi} \int_0^x{\text{exp}(-t^2)dt}` | + +-----------------------+---------------------------------------------------------------+ + | erfc(x) | :math:`1 - \text{erf}(x)` | + +-----------------------+---------------------------------------------------------------+ + | exp(x) | :math:`e^x` | + +-----------------------+---------------------------------------------------------------+ + | floor(x) | Largest integer value not larger than :math:`x` | + +-----------------------+---------------------------------------------------------------+ + | hypot(x,y) | :math:`\sqrt{x^2 + y^2}` | + +-----------------------+---------------------------------------------------------------+ + | ln(x) | :math:`\ln x` | + +-----------------------+---------------------------------------------------------------+ + | log(x) | :math:`\log_{10} x` | + +-----------------------+---------------------------------------------------------------+ + | maxp(x,y) | Takes the maximum between :math:`x` and :math:`y` | + +-----------------------+---------------------------------------------------------------+ + | minp(x,y) | Takes the minimum between :math:`x` and :math:`y` | + +-----------------------+---------------------------------------------------------------+ + | mod(x,y) | Gives the remainder of :math:`x` divided by :math:`y` | + +-----------------------+---------------------------------------------------------------+ + | pi | Ratio of the circumference of a circle and its diameter. | + +-----------------------+---------------------------------------------------------------+ + | rand | Gives a vector of uniformly distributed random numbers | + | | from 0 to 1. | + +-----------------------+---------------------------------------------------------------+ + | rnorm(x,y) | Gives a vector of Gaussian random numbers distributed as | + | | :math:`N(x,y)`. Note that if :math:`x` and :math:`y` are | + | | vectors, each number generated will a different mean and | + | | variance according to the arguments. | + +-----------------------+---------------------------------------------------------------+ + | shift(x,s) | Shifts the values in the input vector :math:`x` by the number | + | | of positions given by :math:`s`. Note that :math:`s` must be | + | | a scalar. | + +-----------------------+---------------------------------------------------------------+ + | sin(x) | :math:`\sin x` | + +-----------------------+---------------------------------------------------------------+ + | sqr(x) | :math:`x^2` | + +-----------------------+---------------------------------------------------------------+ + | sqrt(x) | :math:`\sqrt{x}` | + +-----------------------+---------------------------------------------------------------+ + | tan(x) | :math:`\tan x` | + +-----------------------+---------------------------------------------------------------+ + + +.. tabularcolumns:: |p{0.4\linewidth}|p{0.4\linewidth}| .. _CHDDJEHH: - .. table:: Examples of source waveform expressions. - ============================================= ======================================================================================================================= - Expression Meaning - ============================================= ======================================================================================================================= - q = 20e-9*sin(2*pi*10*x) A 10-Hz sine wave with 20 nAm amplitude - q = 20e-9*sin(2*pi*2*x)*sin(2*pi*10*x) A 10-Hz 20-nAm sine wave, amplitude modulated sinusoidally at 2 Hz. - q = 20e-9*cosw(t,100,100,100) :math:`\cos^2`-shaped pulse, centered at :math:`t` = 100 ms with 100 ms leading and trailing slopes, 20 nAm amplitude. - q = 30e-9*(t > 0)*(t <* 300)*sin(2*pi*20*x) 20-Hz sine wave, 30 nAm amplitude, cropped in time to 0...300 ms. - ============================================= ======================================================================================================================= + +---------------------------------------------+-------------------------------------------------------------+ + | Expression | Meaning | + +---------------------------------------------+-------------------------------------------------------------+ + | q = 20e-9*sin(2*pi*10*x) | A 10-Hz sine wave with 20 nAm amplitude | + +---------------------------------------------+-------------------------------------------------------------+ + | q = 20e-9*sin(2*pi*2*x)*sin(2*pi*10*x) | A 10-Hz 20-nAm sine wave, amplitude modulated | + | | sinusoidally at 2 Hz. | + +---------------------------------------------+-------------------------------------------------------------+ + | q = 20e-9*cosw(t,100,100,100) | :math:`\cos^2`-shaped pulse, centered at :math:`t` = 100 ms | + | | with 100 ms leading and trailing slopes, 20 nAm amplitude | + +---------------------------------------------+-------------------------------------------------------------+ + | q = 30e-9*(t > 0)*(t <* 300)*sin(2*pi*20*x)| 20-Hz sine wave, 30 nAm amplitude, cropped in time to | + | | 0...300 ms. | + +---------------------------------------------+-------------------------------------------------------------+ .. _CHDEDHCG: -- 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
