[med-svn] [python-mne] 286/376: fixing manual
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:23:07 UTC 2015
This is an automated email from the git hooks/post-receive script.
yoh pushed a commit to annotated tag v0.1
in repository python-mne.
commit 466d6468a06e50ec3cb31a8f7130035758414bd5
Author: Emily Ruzich <emilyr at nmr.mgh.harvard.edu>
Date: Thu Jun 2 10:39:29 2011 -0400
fixing manual
---
doc/source/manual/matlab.rst | 586 +++++++++++++++++++++++++++----------------
1 file changed, 375 insertions(+), 211 deletions(-)
diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst
index b8a44f7..765f55e 100755
--- a/doc/source/manual/matlab.rst
+++ b/doc/source/manual/matlab.rst
@@ -759,122 +759,170 @@ The documented structures are:
.. table:: The trans structure.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- ======== ============== =====================================================================================================================================================================
- Field Data type Description
- ======== ============== =====================================================================================================================================================================
- from int32 The source coordinate frame, see :ref:`BGBJHCGD`. Look for entries starting with FIFFV_COORD or FIFFV_MNE_COORD.
- to int32 The destination coordinate frame.
- trans double(4,4) The 4-by-4 coordinate transformation matrix. This operates from augmented position column vectors given in *from* coordinates to give results in *to* coordinates.
- ======== ============== =====================================================================================================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | from | int32 | The source coordinate frame, see :ref:`BGBJHCGD`. Look |
+ | | | for entries starting with FIFFV_COORD or FIFFV_MNE_COORD.|
+ +---------------------------+-----------+----------------------------------------------------------+
+ | to | int32 | The destination coordinate frame. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | trans |double(4,4)| The 4-by-4 coordinate transformation matrix. This |
+ | | | operates from augmented position column vectors given in |
+ | | | *from* coordinates to give results in *to* coordinates. |
+ +---------------------------+-----------+----------------------------------------------------------+
+
.. _BGBHDEDG:
.. table:: The dig structure.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- ======== ============ ==========================================================================================================================
- Field Data type Description
- ======== ============ ==========================================================================================================================
- kind int32 The type of digitizing point. Possible values are listed in :ref:`BGBJHCGD`. Look for entries starting with FIFF_POINT.
- ident int32 Identifier for this point.
- r single(3) The location of this point.
- ======== ============ ==========================================================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | kind | int32 | The type of digitizing point. Possible values are listed |
+ | | | in :ref:`BGBJHCGD`. Look for entries starting with |
+ | | | FIFF_POINT. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | ident | int32 | Identifier for this point. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | r | single(3) | The location of this point. |
+ +---------------------------+-----------+----------------------------------------------------------+
+
.. _BGBGBEBH:
.. table:: The coildef structure. For more detailed information, see :ref:`BJEIAEIE`.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- ============== ======================= ========================================================================================
- Field Data type Description
- ============== ======================= ========================================================================================
- class double The coil (or electrode) class
- id double The coil (or electrode) id
- accuracy double Representation accuracy
- 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 [m] and normal
- FV struct Contains the faces and vertices which can be used to draw the coil for visualization.
- ============== ======================= ========================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | class | double | The coil (or electrode) class. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | id | double | The coil (or electrode) id. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | accuracy | double | Representation accuracy. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | num_points | double | Number of integration points. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | size | double | Coil size. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | baseline | double | Coil baseline. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | description | char(*) | Coil description. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | coildefs | double | Each row contains the integration point weight, followed |
+ | |(num_points| by location [m] and normal. |
+ | |,7) | |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | FV | struct | Contains the faces and vertices which can be used to |
+ | | | draw the coil for visualization. |
+ +---------------------------+-----------+----------------------------------------------------------+
+
.. _BGBIABGD:
.. table:: The ch structure.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- ============== ============== =======================================================================================================================================================================================================================================================================================================================================================
- Field Data type Description
- ============== ============== =======================================================================================================================================================================================================================================================================================================================================================
- scanno int32 Scanning order number, starting from 1.
- logno int32 Logical channel number, conventions in the usage of this number vary.
- 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 [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 [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.
- coil_def coildef The coil definition structure. This is present only if mne_add_coil_defs has been successfully called.
- ============== ============== =======================================================================================================================================================================================================================================================================================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | scanno | int32 | Scanning order number, starting from 1. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | logno | int32 | Logical channel number, conventions in the usage of this |
+ | | | number vary. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | 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 [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 [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. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | coil_def | coildef | The coil definition structure. This is present only if |
+ | | | mne_add_coil_defs has been successfully called. |
+ +---------------------------+-----------+----------------------------------------------------------+
+
.. _BGBCJHJB:
.. table:: The proj structure.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- ========= =============== =========================================================================================================================================================
- Field Data type Description
- ========= =============== =========================================================================================================================================================
- kind int32 The type of the projection item. Possible values are listed in :ref:`BGBJHCGD`. Look for entries starting with FIFFV_PROJ_ITEM or FIFFV_MNE_PROJ_ITEM.
- active int32 Is this item active, i.e. , applied or about to be applied to the data.
- data named matrix The projection vectors. The column names indicate the names of the channels associated to the elements of the vectors.
- ========= =============== =========================================================================================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | kind | int32 | The type of the projection item. Possible values are |
+ | | | listed in :ref:`BGBJHCGD`. Look for entries starting |
+ | | | with FIFFV_PROJ_ITEM or FIFFV_MNE_PROJ_ITEM. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | active | int32 | Is this item active, i.e., applied or about to be |
+ | | | applied to the data. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | data | named | The projection vectors. The column names indicate the |
+ | | matrix | names of the channels associated to the elements of the |
+ | | | vectors. |
+ +---------------------------+-----------+----------------------------------------------------------+
+
.. _BGBJDIFD:
.. table:: The comp structure.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- ================== =============== ===========================================================================================================================================================================================================
- Field Data type Description
- ================== =============== ===========================================================================================================================================================================================================
- 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.
- data named matrix The compensation data matrix. The row_names list the names of the channels to which this compensation applies and the col_names the compensation channels. For more information, see :ref:`BEHDDFBI`.
- ================== =============== ===========================================================================================================================================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | 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. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | data | named | The compensation data matrix. The row_names list the |
+ | | matrix | names of the channels to which this compensation applies |
+ | | | and the col_names the compensation channels. For more |
+ | | | information, see :ref:`BEHDDFBI`. |
+ +---------------------------+-----------+----------------------------------------------------------+
.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|
@@ -882,30 +930,44 @@ The documented structures are:
.. table:: The meas info structure.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- ============= ============== =====================================================================================================================
- Field Data type Description
- ============= ============== =====================================================================================================================
- file_id id The fif ID of the measurement file.
- 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 [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.
- ============= ============== =====================================================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | file_id | id | The fif ID of the measurement file. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | 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 [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. |
+ +---------------------------+-----------+----------------------------------------------------------+
.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|
@@ -913,36 +975,82 @@ The documented structures are:
.. table:: The surf structure.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- =============== ================== ============================================================================================================================================================================================================================================================================
- Field Data type Description
- =============== ================== ============================================================================================================================================================================================================================================================================
- id int32 The surface ID
- sigma double The electrical conductivity of the compartment bounded by this surface. This field is present in BEM surfaces only.
- np int32 Number of vertices on the surface
- ntri int32 Number of triangles on the surface
- coord_frame int32 Coordinate frame in which the locations and orientations are expressed.
- rr double(np,3) The vertex locations
- nn double(np,3) The vertex normals. If derived surface data was not requested, this is empty.
- tris int32(ntri,3) Vertex numbers of the triangles in counterclockwise order as seen from the outside.
- nuse int32 Number of active vertices, *i.e.*, vertices included in a decimated source space.
- inuse int32(np) Which vertices are in use.
- vertno int32(nuse) Indices of the vertices in use.
- curv double(np) Curvature values at the vertices. If curvature information was not requested, this field is empty or absent.
- tri_area double(ntri) The triangle areas in m2.If derived surface data was not requested, this field will be missing.
- tri_cent double(ntri,3) The triangle centroids. If derived surface data was not requested, this field will be missing.
- tri_nn double(ntri,3) The triangle normals. If derived surface data was not requested, this field will be missing.
- nuse_tri int32 Number of triangles in use. This is present only if the surface corresponds to a source space created with the ``--ico`` option.
- use_tris int32(nuse_tri) The vertices of the triangles in use in the complete triangulation. This is present only if the surface corresponds to a source space created with the ``--ico`` option.
- nearest int32(np) This field is present only if patch information has been computed for a source space. For each vertex in the triangulation, these values indicate the nearest active source space vertex.
- nearest_dist double(np) This field is present only if patch information has been computed for a source space. For each vertex in the triangulation, these values indicate the distance to the nearest active source space vertex.
- dist double(np,np) Distances between vertices on this surface given as a sparse matrix. A zero off-diagonal entry in this matrix indicates that the corresponding distance has not been calculated.
- dist_limit double The value given to mne_add_patch_info with the ``--dist`` option, see :ref:`CJAGCDCC`. This value is presently always negative, indicating that only distances between active source space vertices, as indicated by the vertno field of this structure, have been calculated.
- =============== ================== ============================================================================================================================================================================================================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | id | int32 | The surface ID. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | sigma | double | The electrical conductivity of the compartment bounded by|
+ | | | this surface. This field is present in BEM surfaces only.|
+ +---------------------------+-----------+----------------------------------------------------------+
+ | np | int32 | Number of vertices on the surface. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | ntri | int32 | Number of triangles on the surface. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | coord_frame | int32 | Coordinate frame in which the locations and orientations |
+ | | | are expressed. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | rr | double | The vertex locations. |
+ | | (np,3) | |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | nn | double | The vertex normals. If derived surface data was not |
+ | | (np,3) | requested, this is empty. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | tris | int32 | Vertex numbers of the triangles in counterclockwise |
+ | | (ntri,3) | order as seen from the outside. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | nuse | int32 | Number of active vertices, *i.e.*, vertices included in |
+ | | | a decimated source space. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | inuse | int32(np) | Which vertices are in use. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | vertno |int32(nuse)| Indices of the vertices in use. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | curv | double(np)| Curvature values at the vertices. If curvature |
+ | | | information was not requested, this field is empty or |
+ | | | absent. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | tri_area | double | The triangle areas in m2.If derived surface data was not |
+ | | (ntri) | requested, this field will be missing. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | tri_cent | double | The triangle centroids. If derived surface data was not |
+ | | (ntri,3) | requested, this field will be missing. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | tri_nn | double | The triangle normals. If derived surface data was not |
+ | | (ntri,3) | requested, this field will be missing. |
+ +---------------------------+-----------+----------------------------------------------------------+
+
+
+ | nuse_tri | int32 | Number of triangles in use. This is present only if the |
+ | | | surface corresponds to a source space created with the |
+ | | | ``--ico`` option. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | use_tris | int32 | The vertices of the triangles in use in the complete |
+ | | (nuse_tri)| triangulation. This is present only if the surface |
+ | | | corresponds to a source space created with the |
+ | | | ``--ico`` option. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | nearest | int32(np) | This field is present only if patch information has been |
+ | | | computed for a source space. For each vertex in the |
+ | | | triangulation, these values indicate the nearest active |
+ | | | source space vertex. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | nearest_dist | double(np)| This field is present only if patch information has been |
+ | | | computed for a source space. For each vertex in the |
+ | | | triangulation, these values indicate the distance to the |
+ | | | nearest active source space vertex. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | dist | double | Distances between vertices on this surface given as a |
+ | | (np,np) | sparse matrix. A zero off-diagonal entry in this matrix |
+ | | | indicates that the corresponding distance has not been |
+ | | | calculated. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | dist_limit | double | The value given to mne_add_patch_info with the ``--dist``|
+ | | | option, see :ref:`CJAGCDCC`. This value is presently |
+ | | | always negative, indicating that only distances between |
+ | | | active source space vertices, as indicated by the vertno |
+ | | | field of this structure, have been calculated. |
+ +---------------------------+-----------+----------------------------------------------------------+
.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|
@@ -950,25 +1058,34 @@ The documented structures are:
.. table:: The cov structure.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- ========= ================== ======================================================================================================
- Field Data type Description
- ========= ================== ======================================================================================================
- 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).
- 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.
- 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.
- ========= ================== ======================================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | 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). |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | data | double | The covariance matrix. This a double(dim) vector for a |
+ | | (dim,dim) | diagonal covariance matrix. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | 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 | The eigenvectors of the covariance matrix. |
+ | | (dim,dim) | |
+ +---------------------------+-----------+----------------------------------------------------------+
.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|
@@ -976,25 +1093,40 @@ The documented structures are:
.. table:: The fwd structure.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- ============== ==================== =============================================================================================================================================================================================================================
- Field Data type Description
- ============== ==================== =============================================================================================================================================================================================================================
- source_ori int32 Has the solution been computed for the current component normal to the cortex only (1) or all three source orientations (2).
- coord_frame int32 Coordinate frame in which the locations and orientations are expressed.
- nsource int32 Total number of source space points.
- nchan int32 Number of channels.
- sol named matrix The forward solution matrix.
- sol_grad named matrix The derivatives of the forward solution with respect to the dipole location coordinates, see :ref:`BJEFEJJG`. This field is present only if the forward solution was computed with the ``--grad`` option, see :ref:`BJEIGFAE`.
- mri_head_t trans Transformation from the MRI coordinate frame to the (Neuromag) head coordinate frame.
- src surf(*) The description of the source spaces
- source_rr double(nsource,3) The source locations.
- source_nn double(*,3) The source orientations. Number of rows is either nsource (fixed source orientations) or 3*nsource (all source orientations).
- ============== ==================== =============================================================================================================================================================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | source_ori | int32 | Has the solution been computed for the current component |
+ | | | normal to the cortex only (1) or all three source |
+ | | | orientations (2). |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | coord_frame | int32 | Coordinate frame in which the locations and orientations |
+ | | | are expressed. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | nsource | int32 | Total number of source space points. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | nchan | int32 | Number of channels. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | sol | named | The forward solution matrix. |
+ | | matrix | |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | sol_grad | named | The derivatives of the forward solution with respect to |
+ | | matrix | the dipole location coordinates, see :ref:`BJEFEJJG`. |
+ | | | This field is present only if the forward solution was |
+ | | | computed with the ``--grad`` option, see :ref:`BJEIGFAE`.| |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | mri_head_t | trans | Transformation from the MRI coordinate frame to the |
+ | | | (Neuromag) head coordinate frame. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | src | surf(*) | he description of the source spaces. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | source_rr | double | The source locations. |
+ | |(nsource,3)| |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | source_nn |double(*,3)| The source orientations. Number of rows is either |
+ | | | nsource (fixed source orientations) or 3*nsource |
+ | | | (all source orientations). |
+ +---------------------------+-----------+----------------------------------------------------------+
.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|
@@ -1002,34 +1134,66 @@ The documented structures are:
.. table:: The inv structure. Note: The fields proj , whitener , reginv , and noisenorm are filled in by the routine mne_prepare_inverse_operator.
- +--------------------------------+--------------------------------------------------------------+
- | Function | Purpose |
- +================================+==============================================================+
- | fiff_invert_transform | Invert a coordinate transformation structure. |
- +--------------------------------+--------------------------------------------------------------+
- =============== ====================== ==============================================================================================================================================================
- Field Data type Description
- =============== ====================== ==============================================================================================================================================================
- methods int32 Has the solution been computed using MEG data (1), EEG data (2), or both (3).
- source_ori int32 Has the solution been computed for the current component normal to the cortex only (1) or all three source orientations (2)
- 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).
- sing double(nchan) The singular values, *i.e.*, the diagonal values of :math:`\Lambda`, see :ref:`CHDBEHBC`.
- eigen_leads double(*,nchan) The matrix :math:`V`, see :ref:`CHDBEHBC`.
- eigen_fields double(nchan,nchan) The matrix :math:`U^T`, see :ref:`CHDBEHBC`.
- noise_cov cov The noise covariance matrix :math:`C`.
- source_cov cov The source covariance matrix :math:`R`.
- 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
- 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 :math:`\Gamma`, 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).
- =============== ====================== ==============================================================================================================================================================
+ +---------------------------+-----------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +===========================+===========+==========================================================+
+ | methods | int32 | Has the solution been computed using MEG data (1), EEG |
+ | | | data (2), or both (3). |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | source_ori | int32 | Has the solution been computed for the current component |
+ | | | normal to the cortex only (1) or all three source |
+ | | | orientations (2). |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | 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). |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | sing | double | The singular values, *i.e.*, the diagonal values of |
+ | | (nchan) | :math:`\Lambda`, see :ref:`CHDBEHBC`. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | eigen_leads | double | The matrix :math:`V`, see :ref:`CHDBEHBC`. |
+ | | (*,nchan) | |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | eigen_fields | double | The matrix :math:`U^T`, see :ref:`CHDBEHBC`. |
+ | | (nchan, | |
+ | | nchan) | |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | noise_cov | cov | The noise covariance matrix :math:`C`. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | source_cov | cov | The source covariance matrix :math:`R`. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | 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. |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | proj | double | The projection operator computed using projs. |
+ | | (nchan) | |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | whitener | | A sparse matrix containing the noise normalization |
+ | | | factors. Dimension is either nsource (fixed source |
+ | | | orientations) or 3*nsource (all source orientations). |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | reginv | double | The diagonal matrix :math:`\Gamma`, see :ref:`CHDBEHBC`. |
+ | | (nchan) | |
+ +---------------------------+-----------+----------------------------------------------------------+
+ | 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
#############################################
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