mne_types_mne-c.h

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#ifndef _mne_types_h
#define _mne_types_h
/*
 *    Type definitions for the MNE library
 *
 *    Copyright 2001 - 2009
 *
 *    Matti Hamalainen
 *    Athinoula A. Martinos Center for Biomedical Imaging
 *    Massachusetts General Hospital
 *    Charlestown, MA, USA
 *
 *    $Id: mne_types.h 3477 2016-01-14 12:48:00Z msh $
 *
 *    Revision 1.76  2009/03/14 12:37:30  msh
 *    Quite a bit of work for C++ compatibility
 *
 *    Revision 1.75  2009/02/28 17:53:50  msh
 *    Added extra fields to mneWdata and mneStcData with future extensions in mind
 *
 *    Revision 1.74  2009/02/18 02:45:40  msh
 *    Moved to the mneEventList structure, which contains comments per event
 *
 *    Revision 1.73  2009/02/05 04:54:14  msh
 *    Added first_sample_val member to mneRawData
 *
 *    Revision 1.72  2009/01/30 15:20:29  msh
 *    Added code to mask the contents of the digital trigger channel if appropriate
 *
 *    Revision 1.71  2009/01/19 13:08:05  msh
 *    Initialize the MRI structure more completely
 *
 *    Revision 1.70  2008/11/16 20:19:59  msh
 *    Added Talairach transforms
 *    Fixed bugs in MRI reading
 *
 *    Revision 1.69  2008/09/30 11:47:01  msh
 *    Added option to load unprocessed MaxShield data
 *
 *    Revision 1.68  2008/08/15 12:56:49  msh
 *    Added option for discrete source spaces
 *
 *    Revision 1.67  2008/06/16 16:07:09  msh
 *    Added compatibility for the old event file format
 *
 *    Revision 1.66  2008/05/28 10:14:05  msh
 *    Added possibility for a sparse covariance matrix
 *
 *    Revision 1.65  2008/05/26 10:50:10  msh
 *    Changes to accommodate the preweighted lead field basis
 *
 *    Revision 1.64  2008/03/17 18:29:31  msh
 *    Possibility to define the trigger channel with an environment variable
 *    Added mne_compare_filters routine
 *
 *    Revision 1.63  2008/03/15 12:54:46  msh
 *    Handle FIFF_MEAS_DATE appropriately
 *    Copy MNE_PROCESSING_HISTORY to output files as needed
 *    Possibility to add new epochs to raw data epochs previously loaded
 *
 *    Revision 1.62  2008/03/09 01:19:35  msh
 *    Added mne_raw_formatted_time routine
 *    Include first sample to number of omitted samples
 *    Read the FIFF_MEAS_DATE tag
 *
 *    Revision 1.61  2007/04/06 19:07:58  msh
 *    Implemented a new event structure in raw data which will eventually
 *    allow for multiple event lists and comments for the events
 *
 *    Revision 1.60  2007/03/01 04:32:19  msh
 *    Reworked the MRI data structure to be more flexible
 *
 *    Revision 1.59  2007/02/27 17:40:14  msh
 *    Fixed empty row or column handling in mne_create_sparse_rcs and mne_create_sparse_ccs
 *    Fixed memory leak in mne_inverse_io.c
 *    Added new fields to volume source spaces
 *
 *    Revision 1.58  2007/02/26 05:01:29  msh
 *    Added the voxel-RAS coordinate transformation to mneMRIdata
 *    Added routine to set voxels at given RAS coordinate location to given value
 *
 *    Revision 1.57  2007/02/25 14:29:44  msh
 *    Added routines to read mgh and mgz MRI data files.
 *
 *    Revision 1.56  2007/02/23 14:24:47  msh
 *    Made more provisions for volume source spaces.
 *
 *    Revision 1.55  2007/02/20 20:40:40  msh
 *    Match channel names without spaces as well for compatibility with
 *    the new Neuromag channel naming scheme.
 *
 *    Revision 1.54  2007/01/29 21:02:44  msh
 *    Added the additional prior weightings to the inverse operator structure
 *
 *    Revision 1.53  2007/01/09 12:43:08  msh
 *    Added total area member to the mneSourceSpace structure
 *    Compute the total area in mne_add_triangle_data
 *
 *    Revision 1.52  2006/12/08 16:36:36  msh
 *    Added source file name to layout.
 *
 *    Revision 1.51  2006/12/05 21:27:55  msh
 *    Added the SSS stuff to raw data and the covariance matrix
 *
 *    Revision 1.50  2006/11/16 22:46:13  msh
 *    Changed sample number in mneTrigEvent to be a signed integer.
 *
 *    Revision 1.49  2006/10/16 13:39:17  msh
 *    Changed field names in mneMeasDataSet structure
 *
 */
#include <fiff/c/fiff_types.h>
 
#if defined(__cplusplus) 
extern "C" {
#endif
 
/*
 * Complex data
 */
typedef struct {
  float re;
  float im;
} *mneComplex,**mneComplexMatrix,mneComplexRec;
 
typedef struct {
  double re;
  double im;
} *mneDoubleComplex,**mneDoubleComplexMatrix,mneDoubleComplexRec;
 
typedef void (*mneUserFreeFunc)(void *);  /* General purpose */
typedef fiffSparseMatrix mneSparseMatrix;
typedef fiffSparseMatrixRec mneSparseMatrixRec;
 
typedef struct {
  int   vert;           /* Which vertex does this apply to */
  int   *memb_vert;     /* Which vertices constitute the patch? */
  int   nmemb;          /* How many? */
  float area;           /* Area of the patch */
  float ave_nn[3];      /* Average normal */
  float dev_nn;         /* Average deviation of the patch normals from the average normal */
} *mnePatchInfo,mnePatchInfoRec;
 
typedef struct {        /* This is used in the patch definitions */
  int   vert;           /* Number of this vertex (to enable sorting) */
  int   nearest;        /* Nearest 'inuse' vertex */
  float dist;                   /* Distance to the nearest 'inuse' vertex */
  mnePatchInfo patch;           /* The patch information record for the patch this vertex belongs to */
} *mneNearest,mneNearestRec;
 
typedef struct {
  int   *vert;              /* Triangle vertices (pointers to the itris member of the associated mneSurface) */
  float *r1,*r2,*r3;            /* Triangle vertex locations (pointers to the rr member of the associated mneSurface) */
  float r12[3],r13[3];      /* Vectors along the sides */
  float nn[3];          /* Normal vector */
  float area;           /* Area */
  float cent[3];        /* Centroid */
  float ex[3],ey[3];        /* Other unit vectors (used by BEM calculations) */
} *mneTriangle,mneTriangleRec;  /* Triangle data */
 
typedef struct {
  int            valid;                  /* Is the information below valid */
  int            width,height,depth;         /* Size of the stack */
  float          xsize,ysize,zsize;      /* Increments in the three voxel directions */
  float          x_ras[3],y_ras[3],z_ras[3]; /* Directions of the coordinate axes */
  float          c_ras[3];                   /* Center of the RAS coordinates */
  char           *filename;          /* Name of the MRI data file */
} *mneVolGeom,mneVolGeomRec;             /* MRI data volume geometry information like FreeSurfer keeps it */
  
/*
 * Values of the type field in the mneVolumeOrSurface structure
 */
#define MNE_SOURCE_SPACE_UNKNOWN -1
#define MNE_SOURCE_SPACE_SURFACE  1 /* Surface-based source space */
#define MNE_SOURCE_SPACE_VOLUME   2 /* 3D volume source space */
#define MNE_SOURCE_SPACE_DISCRETE 3 /* Discrete points */
 
typedef struct {            /* This defines a source space or a surface */
  int              type;        /* Is this a volume or a surface */
  char             *subject;        /* Name (id) of the subject */
  int              id;          /* Surface id */
  int              coord_frame;     /* Which coordinate system are the data in now */
  /*
   * These relate to the FreeSurfer way
   */
  mneVolGeom       vol_geom;        /* MRI volume geometry information as FreeSurfer likes it */
  void             *mgh_tags;       /* Tags listed in the file */
  /*
   * These are meaningful for both surfaces and volumes
   */
  int              np;          /* Number of vertices */
  float            **rr;        /* The vertex locations */
  float            **nn;        /* Surface normals at these points */
  float            cm[3];       /* Center of mass */
 
  int              *inuse;      /* Is this point in use in the source space */
  int              *vertno;     /* Vertex numbers of the used vertices in the full source space */
  int              nuse;        /* Number of points in use */
 
  int              **neighbor_vert; /* Vertices neighboring each vertex */
  int              *nneighbor_vert; /* Number of vertices neighboring each vertex */
  float            **vert_dist;     /* Distances between neigboring vertices */
  /*
   * These are for surfaces only
   */
  int              ntri;        /* Number of triangles */
  mneTriangle      tris;        /* The triangulation information */
  int              **itris;     /* The vertex numbers */
  float            tot_area;        /* Total area of the surface, computed from the triangles */
 
  int              nuse_tri;        /* The triangulation corresponding to the vertices in use */
  mneTriangle      use_tris;        /* The triangulation information for the vertices in use */
  int              **use_itris;     /* The vertex numbers for the 'use' triangulation */
 
  int              **neighbor_tri;  /* Neighboring triangles for each vertex 
                     * Note: number of entries varies for vertex to vertex */
  int              *nneighbor_tri;  /* Number of neighboring triangles for each vertex */
 
  mneNearest       nearest;     /* Nearest inuse vertex info (number of these is the same as the number vertices) */
  mnePatchInfo     *patches;        /* Patch information (number of these is the same as the number of points in use) */
  int              npatch;      /* How many (should be same as nuse) */
 
  mneSparseMatrix  dist;        /* Distances between the (used) vertices (along the surface). */
  float            dist_limit;      /* Distances above this (in volume) have not been calculated. 
                     * If negative, only used vertices have been considered */
 
  float            *curv;       /* The FreeSurfer curvature values */
  float            *val;        /* Some other values associated with the vertices */
  /*
   * These are for volumes only
   */
  fiffCoordTrans   voxel_surf_RAS_t;/* Transform from voxel coordinate to the surface RAS (MRI) coordinates */
  int              vol_dims[3];     /* Dimensions of the volume grid (width x height x depth) 
                     * NOTE: This will be present only if the source space is a complete 
                     * rectangular grid with unused vertices included */
  float            voxel_size[3];   /* Derived from the above */
  mneSparseMatrix  interpolator;    /* Matrix to interpolate into an MRI volume */
  char             *MRI_volume;     /* The name of the file the above interpolator is based on */
  fiffCoordTrans   MRI_voxel_surf_RAS_t;
  fiffCoordTrans   MRI_surf_RAS_RAS_t;  /* Transform from surface RAS to RAS coordinates in the associated MRI volume */
  int              MRI_vol_dims[3];     /* Dimensions of the MRI volume (width x height x depth) */
  /*
   * Possibility to add user-defined data
   */
  void             *user_data;      /* Anything else we want */
  mneUserFreeFunc  user_data_free;  /* Function to set the above free */
} *mneSurfaceOrVolume,mneSurfaceOrVolumeRec;
/*
 * These are the aliases
 */
typedef mneSurfaceOrVolume mneSourceSpace;
typedef mneSurfaceOrVolume mneSourceVolume;
typedef mneSurfaceOrVolume mneSurface;
typedef mneSurfaceOrVolume mneVolume;
 
typedef mneSurfaceOrVolumeRec mneSourceSpaceRec;
typedef mneSurfaceOrVolumeRec mneSourceVolumeRecRec;
typedef mneSurfaceOrVolumeRec mneSurfaceRec;
typedef mneSurfaceOrVolumeRec mneVolumeRec;
 
//typedef struct {          /* FreeSurfer patches */
//  mneSurface       s;         /* Patch represented as a surface */
//  int              *vert;     /* Vertex numbers in the complete surface*/
//  int              *surf_vert;        /* Which vertex corresponds to each complete surface vertex here? */
//  int              np_surf;       /* How many points on the complete surface? */
//  int              *tri;      /* Which triangles in the complete surface correspond to our triangles? */
//  int              *surf_tri;     /* Which of our triangles corresponds to each triangle on the complete surface? */
//  int              ntri_surf;     /* How many triangles on the complete surface */
//  int              *border;       /* Is this vertex on the border? */
//  int              flat;      /* Is this a flat patch? */
//  void             *user_data;      /* Anything else we want */
//  mneUserFreeFunc  user_data_free;  /* Function to set the above free */
//} *mneSurfacePatch,mneSurfacePatchRec;
 
typedef struct {        /* Matrix specification with a channel list */
  int   nrow;           /* Number of rows */
  int   ncol;           /* Number of columns */
  char  **rowlist;      /* Name list for the rows (may be NULL) */
  char  **collist;      /* Name list for the columns (may be NULL) */
  float **data;                  /* The data itself (dense) */
} *mneNamedMatrix,mneNamedMatrixRec;
 
typedef struct {        /* Matrix specification with a channel list */
  int   nrow;           /* Number of rows (same as in data) */
  int   ncol;           /* Number of columns (same as in data) */
  char  **rowlist;      /* Name list for the rows (may be NULL) */
  char  **collist;      /* Name list for the columns (may be NULL) */
  mneSparseMatrix data;     /* The data itself (sparse) */
} *mneSparseNamedMatrix,mneSparseNamedMatrixRec;
 
typedef struct {        /* Vector specification with a channel list */
  int    nvec;          /* Number of elements */
  char   **names;       /* Name list for the elements */
  float  *data;         /* The data itself */
} *mneNamedVector,mneNamedVectorRec;
 
typedef struct {        /* One linear projection item */
  mneNamedMatrix vecs;          /* The original projection vectors */
  int            nvec;          /* Number of vectors = vecs->nrow */
  char           *desc;         /* Projection item description */
  int            kind;          /* Projection item kind */
  int            active;    /* Is this item active now? */
  int            active_file;   /* Was this item active when loaded from file? */
  int            has_meg;   /* Does it have MEG channels? */
  int            has_eeg;   /* Does it have EEG channels? */
} *mneProjItem,mneProjItemRec;
 
typedef struct {        /* Collection of projection items and the projector itself */
  mneProjItem    *items;        /* The projection items */
  int            nitems;        /* Number of items */
  char           **names;   /* Names of the channels in the final projector */
  int            nch;           /* Number of channels in the final projector */
  int            nvec;          /* Number of vectors in the final projector */
  float          **proj_data;   /* The orthogonalized projection vectors picked and orthogonalized from the original data */
} *mneProjOp,mneProjOpRec;
 
typedef struct {
  int   job;            /* Value of FIFF_SSS_JOB tag */
  int   coord_frame;        /* Coordinate frame */
  float origin[3];      /* The expansion origin */
  int   nchan;          /* How many channels */
  int   out_order;      /* Order of the outside expansion */
  int   in_order;       /* Order of the inside expansion */
  int   *comp_info;     /* Which components are included */
  int   ncomp;          /* How many entries in the above */
  int   in_nuse;        /* How many components included in the inside expansion */
  int   out_nuse;       /* How many components included in the outside expansion */
} *mneSssData,mneSssDataRec;    /* Essential information about SSS */
 
/*
 * The class field in mneCovMatrix can have these values
 */
#define MNE_COV_CH_UNKNOWN  -1  /* No idea */
#define MNE_COV_CH_MEG_MAG   0  /* Axial gradiometer or magnetometer [T] */
#define MNE_COV_CH_MEG_GRAD  1  /* Planar gradiometer [T/m] */
#define MNE_COV_CH_EEG       2  /* EEG [V] */
 
//typedef struct {      /* Covariance matrix storage */
//  int        kind;        /* Sensor or source covariance */
//  int        ncov;        /* Dimension */
//  int        nfree;       /* Number of degrees of freedom */
//  int        nproj;       /* Number of dimensions projected out */
//  int        nzero;       /* Number of zero or small eigenvalues */
//  char       **names;     /* Names of the entries (optional) */
//  double     *cov;        /* Covariance matrix in packed representation (lower triangle) */
//  double     *cov_diag;       /* Diagonal covariance matrix */
//  mneSparseMatrix cov_sparse;   /* A sparse covariance matrix
//               * (Note: data are floats in this which is an inconsistency) */
//  double     *lambda;     /* Eigenvalues of cov */
//  double     *inv_lambda; /* Inverses of the square roots of the eigenvalues of cov */
//  float      **eigen;     /* Eigenvectors of cov */
//  double     *chol;       /* Cholesky decomposition */
//  mneProjOp  proj;        /* The projection which was active when this matrix was computed */
//  mneSssData sss;     /* The SSS data present in the associated raw data file */
//  int        *ch_class;       /* This will allow grouping of channels for regularization (MEG [T/m], MEG [T], EEG [V] */
//  char       **bads;      /* Which channels were designated bad when this noise covariance matrix was computed? */
//  int        nbad;        /* How many of them */
//} *mneCovMatrix,mneCovMatrixRec;
 
//typedef struct {      /* A forward solution */
//  char           *fwdname;    /* Name of the file this was loaded from */
//  fiffId         meas_id;       /* The assosiated measurement ID */
//  mneSourceSpace *spaces; /* The source spaces */
//  int            nspace;  /* Number of source spaces */
//  fiffCoordTrans mri_head_t;  /* MRI <-> head coordinate transformation */
//  fiffCoordTrans meg_head_t;    /* MEG <-> head coordinate transformation */
//  int            methods; /* EEG, MEG or EEG+MEG (see mne_fiff.h) */
//  int            coord_frame; /* The coordinate frame employed in the forward calculations */
//  int            source_ori;  /* Fixed or free source orientations */
//  float          **rr_source; /* The active source points */
//  float          **nn_source; /* The source orientations
//               * (These are equal to the cortex normals
//               * in the fixed orientation case) */
//  int            nsource; /* Number of source (recalculated for convenience) */
//  fiffChInfo     chs;     /* The channel list */
//  int            nch;     /* Number of channels */
//  mneNamedMatrix fwd;         /* The forward solution (may be whitened) */
//  mneNamedMatrix fwd_proc;    /* This is an alternate matrix for a processed forward matrix (linear projection
//               * and whitening) As a rule, this field is not used but rater the operations are
//               * applied to the field fwd itself */
//  float          *patch_areas;  /* Contains the patch areas if the CSD transformation has been applied */
//  int            fwd_whitened;    /* Has the noise covariance been applied to the field fwd? */
//  mneCovMatrix   noise_cov;   /* The noise covariance matrix employed in whitening */
//  mneProjOp      proj;        /* Associated projection operator */
//} *mneForwardSolution,mneForwardSolutionRec;
 
//typedef struct {                /* An inverse operator */
//  fiffId         meas_id;                 /* The assosiated measurement ID */
//  mneSourceSpace *spaces;           /* The source spaces */
//  int            nspace;            /* Number of source spaces */
//  fiffCoordTrans meg_head_t;              /* MEG device <-> head coordinate transformation */
//  fiffCoordTrans mri_head_t;            /* MRI device <-> head coordinate transformation */
//  int            methods;           /* EEG, MEG or EEG+MEG (see mne_fiff.h) */
//  int            nchan;                 /* Number of measurement channels */
//  int            nsource;           /* Number of source points */
//  int            fixed_ori;             /* Fixed source orientations? */
//  float          **rr_source;           /* The active source points */
//  float          **nn_source;           /* The source orientations
//                     * (These are equal to the cortex normals
//                     * in the fixed orientation case) */
//  int            coord_frame;             /* Which coordinates are the locations and orientations given in? */
//  mneCovMatrix   sensor_cov;            /* Sensor covariance matrix */
//  int            nave;                  /* Number of averaged responses (affects scaling of the noise covariance) */
//  int            current_unit;          /* This can be FIFF_UNIT_AM, FIFF_UNIT_AM_M2, FIFF_UNIT_AM_M3 */
//  mneCovMatrix   source_cov;            /* Source covariance matrix */
//  mneCovMatrix   orient_prior;              /* Orientation prior applied */
//  mneCovMatrix   depth_prior;           /* Depth-weighting prior applied */
//  mneCovMatrix   fMRI_prior;            /* fMRI prior applied */
//  float          *sing;                 /* Singular values of the inverse operator */
//  mneNamedMatrix eigen_leads;           /* The eigen leadfields */
//  int            eigen_leads_weighted;    /* Have the above been already weighted with R^0.5? */
//  mneNamedMatrix eigen_fields;              /* Associated field patterns */
//  float          trace_ratio;           /* tr(GRG^T)/tr(C) */
//  mneProjOp      proj;                  /* The associated projection operator */
//} *mneInverseOperator,mneInverseOperatorRec;
 
typedef struct {        /* For storing the wdata */
  int   id;         /* Surface id these data belong to */
  int   kind;           /* What kind of data */
  float lat;            /* Latency */
  int   nvert;          /* Number of vertices */
  int   *vertno;        /* Vertex numbers */
  float *vals;          /* The values */
} *mneWdata,mneWdataRec;
 
typedef struct {
  int   id;         /* Surface id these data belong to */
  int   kind;           /* What kind of data */
  float tmin;           /* First time */
  float tstep;          /* Step between times */
  int   ntime;          /* Number of times */
  int   nvert;          /* Number of vertices */
  int   *vertno;        /* The vertex numbers */
  float **data;         /* The data, time by time */
} *mneStcData,mneStcDataRec;
 
//typedef struct {      /* Information about raw data in fiff file */
//  char          *filename;    /* The name of the file this comes from */
//  fiffId        id;       /* Measurement id from the file */
//  int           nchan;        /* Number of channels */
//  fiffChInfo    chInfo;       /* Channel info data  */
//  int           coord_frame;  /*
//               * Which coordinate frame are the
//               * positions defined in?
//               */
//  fiffCoordTrans trans;           /* This is the coordinate transformation
//               * FIFF_COORD_HEAD <--> FIFF_COORD_DEVICE
//               */
//  float         sfreq;        /* Sampling frequency */
//  float         lowpass;  /* Lowpass filter setting */
//  float         highpass;       /* Highpass filter setting */
//  fiffTimeRec   start_time;   /* Starting time of the acquisition
//               * taken from the meas date
//               * or the meas block id
//               * whence it may be inaccurate. */
//  int           buf_size; /* Buffer size in samples */
//  int           maxshield_data; /* Are these unprocessed MaxShield data */
//  fiffDirEntry  rawDir;       /* Directory of raw data tags
//               * These may be of type
//               *       FIFF_DATA_BUFFER
//               *       FIFF_DATA_SKIP
//               *       FIFF_DATA_SKIP_SAMP
//               *       FIFF_NOP
//               */
//  int           ndir;     /* Number of tags in the above
//               * directory */
//} mneRawInfoRec, *mneRawInfo;
 
typedef struct {        /* Spatiotemporal map */
  int kind;         /* What kind of data */
  int coord_frame;      /* Coordinate frame for vector values */
  int nvert;            /* Number of vertex values */
  int ntime;            /* Number of time points */
  int nval_vert;        /* Number of values per vertex */
  float tmin;           /* First time point */
  float tstep;          /* Step between the time points */
  int   *vertno;        /* Vertex numbers in the full triangulation (starting with zero) */
  float **data;         /* The data values (time by time) */
} mneMapRec, *mneMap;
 
typedef struct {                     /* Plotter layout port definition */
  int   portno;                      /* Running number of this viewport */
  int   invert;                      /* Invert the signal coming to this port */
  float xmin,xmax,ymin,ymax;                 /* Limits */
  char  *names;                      /* Channels to go into this port (one line, separated by colons) */
  int   match;                       /* Does this port match with our present channel? */
} mneLayoutPortRec,*mneLayoutPort;
 
typedef struct {                     /* Plotter layout */
  char          *name;                   /* File where this came from */
  float         xmin,xmax,ymin,ymax;             /* The VDC limits */
  float         cxmin,cxmax,cymin,cymax;         /* The confined VDC limits */
  int           nport;                   /* Number of viewports */
  mneLayoutPort ports;                   /* Array of viewports */
  int           **match;                 /* Matching matrix */
  int           nmatch;                  /* How many channels in matching matrix */
} mneLayoutRec,*mneLayout;
 
/*
 * The following relate to high-level handling of raw data
 */
#define MNE_CH_SELECTION_UNKNOWN 0
#define MNE_CH_SELECTION_FILE    1
#define MNE_CH_SELECTION_USER    2
 
typedef struct {
  char *name;           /* Name of this selection */
  char **chdef;         /* Channel definitions (may contain regular expressions) */
  int  ndef;            /* How many of them */
  char **chspick;       /* Translated into channel names using the present data */
  char **chspick_nospace;   /* The same without spaces */
  int  *pick;           /* These are the corresponding channels in the raw data 
                   (< 0 indicates missing) */
  int  *pick_deriv;     /* These are the corresponding derivations in the raw data */
  int  nderiv;          /* How many derivations in the above */
  int  *ch_kind;        /* Kinds of the channels corresponding to picks (< 0 indicates missing) */
  int  nchan;           /* How many picked channels? */
  int  kind;            /* Loaded from file or created here? */
} *mneChSelection,mneChSelectionRec;
 
typedef struct {
  char        *name;        /* Name of this set */
  mneChSelection *sels;     /* These are the selections */
  int         nsel;     /* How many */
  int         current;      /* Which is active now? */
} *mneChSelectionSet, mneChSelectionSetRec;
 
typedef struct {
  unsigned int from;        /* Source transition value */
  unsigned int to;      /* Destination transition value */
  int          sample;      /* Sample number */
  int          show;        /* Can be used as desired */
  int          created_here;    /* Was this event created in the program */
  char         *comment;    /* Event comment */
} *mneEvent,mneEventRec;
 
typedef struct {        /* List of the above. */
  mneEvent     *events;
  int          nevent;
} *mneEventList,mneEventListRec;
 
typedef struct {
  int   filter_on;      /* Is it on? */
  int   size;           /* Length in samples (must be a power of 2) */
  int   taper_size;     /* How long a taper in the beginning and end */
  float highpass;       /* Highpass in Hz */
  float highpass_width;     /* Highpass transition width in Hz */
  float lowpass;        /* Lowpass in Hz */
  float lowpass_width;      /* Lowpass transition width in Hz */
  float eog_highpass;       /* EOG highpass in Hz */
  float eog_highpass_width; /* EOG highpass transition width in Hz */
  float eog_lowpass;        /* EOG lowpass in Hz */
  float eog_lowpass_width;  /* EOG lowpass transition width in Hz */
} *mneFilterDef,mneFilterDefRec;
 
//typedef struct {
//  fiffDirEntry ent;       /* Where is this in the file (file bufs only, pointer to info) */
//  int   firsts,lasts;     /* First and last sample */
//  int   ntaper;           /* For filtered buffers: taper length */
//  int   ns;           /* Number of samples (last - first + 1) */
//  int   nchan;            /* Number of channels */
//  int   is_skip;      /* Is this a skip? */
//  float **vals;           /* Values (null if not in memory) */
//  int   valid;            /* Are the data meaningful? */
//  int   *ch_filtered;     /* For filtered buffers: has this channel filtered already */
//  int   comp_status;      /* For raw buffers: compensation status */
//} *mneRawBufDef,mneRawBufDefRec;
 
/*
 * CTF compensation stuff
 */
#define MNE_CTFV_NOGRAD           0
#define MNE_CTFV_GRAD1            1
#define MNE_CTFV_GRAD2            2
#define MNE_CTFV_GRAD3            3
/*
 * 4D compensation stuff
 */
#define MNE_4DV_COMP1           101
 
typedef struct {
  int             kind;          /* The compensation kind (CTF) */
  int             mne_kind;      /* Our kind */
  int             calibrated;        /* Are the coefficients in the file calibrated already? */
  mneNamedMatrix  data;              /* The compensation data */
  mneSparseMatrix presel;            /* Apply this selector prior to compensation */
  mneSparseMatrix postsel;       /* Apply this selector after compensation */
  float           *presel_data;      /* These are used for the intermediate results in the calculations */
  float           *comp_data;
  float           *postsel_data;
} *mneCTFcompData,mneCTFcompDataRec;
 
typedef struct {
  mneCTFcompData *comps;    /* All available compensation data sets */
  int            ncomp;     /* How many? */
  fiffChInfo     chs;       /* Channel information */
  int            nch;       /* How many of the above */
  mneCTFcompData undo;      /* Compensation data to undo the current compensation before applying current */
  mneCTFcompData current;   /* The current compensation data composed from the above 
                 * taking into account channels presently available */
} *mneCTFcompDataSet,mneCTFcompDataSetRec;
 
typedef struct {                /* One item in a derivation data set */
  char                 *filename;       /* Source file name */
  char                 *shortname;      /* Short nickname for this derivation */
  mneSparseNamedMatrix deriv_data;  /* The derivation data itself */
  int                  *in_use;     /* How many non-zero elements on each column of the derivation data 
                     * (This field is not always used) */
  int                  *valid;      /* Which of the derivations are valid considering the units of the input 
                     * channels (This field is not always used) */
  fiffChInfo           chs;     /* First matching channel info in each derivation */
} *mneDeriv,mneDerivRec;
 
typedef struct {                /* A collection of derivations */
  int      nderiv;              /* How many? */
  mneDeriv *derivs;         /* Pointers to the items */
} *mneDerivSet,mneDerivSetRec;
 
typedef struct {            /* A comprehensive raw data structure */
  char             *filename;           /* This is our file */
  fiffFile         file;            
  mneRawInfo       info;            /* Loaded using the mne routines */
  char             **ch_names;      /* Useful to have the channel names as a single list */
  char             **badlist;       /* Bad channel names */
  int              nbad;        /* How many? */
  int              *bad;        /* Which channels are bad? */
  mneRawBufDef     bufs;        /* These are the data */
  int              nbuf;        /* How many? */
  mneRawBufDef     filt_bufs;           /* These are the filtered ones */
  int              nfilt_buf;
  int              first_samp;          /* First sample? */
  int              omit_samp;       /* How many samples of skip omitted in the beginning */
  int              omit_samp_old;       /* This is the value omit_samp would have in the old versions */
  int              nsamp;           /* How many samples in total? */
  float            *first_sample_val;   /* Values at the first sample (for dc offset correction before filtering) */
  mneProjOp        proj;        /* Projection operator */
  mneSssData       sss;         /* SSS data found in this file */
  mneCTFcompDataSet comp;       /* Compensation data */
  int              comp_file;           /* Compensation status of these raw data in file */
  int              comp_now;            /* Compensation status of these raw data in file */
  mneFilterDef     filter;      /* Filter definition */
  void             *filter_data;        /* This can be whatever the filter needs */
  mneUserFreeFunc  filter_data_free;    /* Function to free the above */
  mneEventList     event_list;      /* Trigger events */
  unsigned int     max_event;           /* Maximum event number in usenest */
  char             *dig_trigger;        /* Name of the digital trigger channel */
  unsigned int     dig_trigger_mask;    /* Mask applied to digital trigger channel before considering it */
  float            *offsets;        /* Dc offset corrections for display */
  void             *ring;           /* The ringbuffer (structure is of no
                     * interest to us) */
  void             *filt_ring;          /* Separate ring buffer for filtered data */
  mneDerivSet      deriv;           /* Derivation data */
  mneDeriv         deriv_matched;   /* Derivation data matched to this raw data and 
                     * collected into a single item */
  float            *deriv_offsets;  /* Dc offset corrections for display of the derived channels */
  void             *user;           /* Whatever */
  mneUserFreeFunc  user_free;       /* How this is freed */
} *mneRawData,mneRawDataRec;        
 
typedef struct {         /* Data associated with MNE computations for each mneMeasDataSet */
  float **datap;         /* Projection of the whitened data onto the field eigenvectors */
  float **predicted;         /* The predicted data */
  float *SNR;            /* Estimated power SNR as a function of time */
  float *lambda2_est;        /* Regularization parameter estimated from available data */
  float *lambda2;                /* Regularization parameter to be used (as a function of time) */      
} *mneMneData,mneMneDataRec;
 
typedef struct {         /* One data set, used in mneMeasData */
  /*
   * These are unique to each data set
   */ 
  char            *comment;  /* Comment associated with these data */
  float           **data;    /* The measured data */
  float           **data_proj;   /* Some programs maybe interested in keeping the data after SSP separately */
  float           **data_filt;   /* Some programs maybe interested in putting a filtered version here */
  float           **data_white;  /* The whitened data */
  float           *stim14;   /* Data from the digital stimulus channel */
  int             first;     /* First sample index for raw data processing */
  int             np;        /* Number of times */
  int             nave;      /* Number of averaged responses */
  int             kind;      /* Which aspect of data */
  float           tmin;      /* Starting time */
  float           tstep;     /* Time step */
  float           *baselines;    /* Baseline values currently applied to the data */
  mneMneData      mne;       /* These are the data associated with MNE computations */
  void            *user_data;    /* Anything else we want */
  mneUserFreeFunc user_data_free;/* Function to set the above free */
} *mneMeasDataSet,mneMeasDataSetRec;
 
typedef struct {         /* Measurement data representation in MNE calculations */
  /*
   * These are common to all data sets
   */
  char               *filename;  /* The source file name */
  fiffId             meas_id;    /* The id from the measurement file */
  fiffTimeRec        meas_date;  /* The measurement date from the file */
  fiffChInfo         chs;    /* The channel information */
  fiffCoordTrans     meg_head_t; /* MEG device <-> head coordinate transformation */
  fiffCoordTrans     mri_head_t; /* MRI device <-> head coordinate transformation 
                    (duplicated from the inverse operator or loaded separately) */
  float              sfreq;  /* Sampling frequency */
  int                nchan;  /* Number of channels */
  float              highpass;   /* Highpass filter setting */ 
  float              lowpass;    /* Lowpass filter setting */ 
  mneProjOp          proj;   /* Associated projection operator (useful if inverse operator is not included) */
  mneCTFcompDataSet  comp;   /* The software gradient compensation data */
  mneInverseOperator op;     /* Associated inverse operator */
  mneNamedMatrix     fwd;    /* Forward operator for dipole fitting */
  mneRawData         raw;    /* This will be non-null if the data stems from a raw data file */
  mneChSelection     chsel;  /* Channel selection for raw data */
  char               **badlist;  /* Bad channel names */
  int                nbad;   /* How many? */
  int                *bad;   /* Which channels are bad? */
  /*
   * These are the data sets loaded
   */
  int                ch_major;   /* Rows are channels rather than times */
  mneMeasDataSet     *sets;  /* All loaded data sets */
  int                nset;   /* How many */
  mneMeasDataSet     current;    /* Which is the current one */
} *mneMeasData,mneMeasDataRec;
 
typedef struct {        /* Identifier for the automatic parcellation */
  char  *name;          /* Name of this area */
  int   index;          /* Index in the parcellation */
  int   flag;           /* Flag read from  the color table (whatever it means) */
  float r,g,b,alpha;        /* The color values */
  int   *vert;              /* The vertices belonging to this one */
  int   nvert;
} *mneParc,mneParcRec;
 
typedef struct {        /* A set of the above */
  int       *vert;      /* The assignment of each vertex */
  int       nvert;      /* How many */
  mneParc   *parcs;     /* The 'parcels' */
  int       nparc;
} *mneParcSet,mneParcSetRec;
 
typedef struct {
  mneParcSet   lh_parc;
  mneParcSet   rh_parc;
} *mneParcData,mneParcDataRec;  /* This is the complete parcellation data */
 
/*
 * The following are included for reading and writing MRI data in the mgh and mgz formats
 */
#define MNE_MRI_VERSION       1
#define MNE_MRI_UCHAR         0
#define MNE_MRI_INT           1
#define MNE_MRI_LONG          2
#define MNE_MRI_FLOAT         3
#define MNE_MRI_SHORT         4
#define MNE_MRI_BITMAP        5
#define MNE_MRI_TENSOR        6
 
#define MNE_MRI_ALL_FRAMES    -1         /* Load all frames */
#define MNE_MRI_NO_FRAMES     -2         /* Do not load data at all */
 
typedef union {
  unsigned char uval;
  short         sval;
  int           ival;
  float         fval;
} mneMRIvoxelVal;
 
typedef union {
  unsigned char   ***uslices;                /* Different types of voxels */
  short           ***sslices;
  int             ***islices;
  float           ***fslices;
} mneMRIvoxels;
 
typedef struct {
  int             type;              /* Data type duplicated from mneMRIdata */
  int             width;             /* Size of the stack duplicated from mneMRIdata*/
  int             height;
  int             depth;
  void            *data;             /* These are the actual voxels stored sequentially */
  int             nbytes;            /* How many bytes in data (just a convenience) */
  mneMRIvoxels    voxels;            /* Different types of voxels */
  int             frame;             /* Which frame is this in the original data */
  void            *user_data;                /* Anything else we want */
  mneUserFreeFunc user_data_free;            /* Function to set the above free */
} *mneMRIvolume,mneMRIvolumeRec;         /* One volume of data */
 
typedef struct {
  char           *filename;                  /* Name of the source file */
  int            version;                /* Version number of the data file */
  int            width;                  /* Size of the stack */
  int            height;
  int            depth;
  int            nframes;            /* Number of frames in the original */
  int            dof;
  int            ras_good;                   /* Indicates that the values below are good */
  float          xsize,ysize,zsize;      /* Increments in the three voxel directions */
  float          x_ras[3],y_ras[3],z_ras[3]; /* these are the RAS distances across the whole volume */
  float          c_ras[3];                   /* Center of the RAS coordinates 
                          * This is irrelevant to the MNE software because we work in
                          * surface RAS coordinates */
  fiffCoordTrans voxel_surf_RAS_t;           /* Transform from voxel coordinate to the surface RAS (MRI) coordinates */
  fiffCoordTrans surf_RAS_RAS_t;             /* Transform from surface RAS to RAS (nonzero origin) coordinates */
  fiffCoordTrans head_surf_RAS_t;        /* Transform from MEG head coordinates to surface RAS */
  fiffCoordTrans RAS_MNI_tal_t;              /* Transform from RAS (nonzero origin) to MNI Talairach coordinates */
  fiffCoordTrans MNI_tal_tal_gtz_t;          /* Transform MNI Talairach to FreeSurfer Talairach coordinates (z > 0) */
  fiffCoordTrans MNI_tal_tal_ltz_t;          /* Transform MNI Talairach to FreeSurfer Talairach coordinates (z < 0) */
  int            type;                       /* Data type for voxels */
  mneMRIvolume   *volumes;               /* The volumes loaded */
  int            nvol;                   /* How many loaded volumes */
  int            current_vol;            /* Which volume is the current destination for modifications */
  float          TR;                 /* Recovery time */
  float          TE;                 /* Echo time time */
  float          TI;                 /* Inversion time */
  float          flip_angle;             /* Flip angle */
  float          fov;                /* Field of view */
  void            *tags;             /* The format of the tag information is kept private */
  void            *user_data;                /* Anything else we want */
  mneUserFreeFunc user_data_free;            /* Function to set the above free */
} *mneMRIdata,mneMRIdataRec;             /* MRI data description suitable for handling mgh and mgz data files */
 
/*
 * Wavelet transform structures
 */
typedef struct {
  float sfreq;          /* The sampling frequency */
  int   nfreq;              /* How many frequencies */
  float **W;            /* The corresponding wavelets */
  float **W_power;              /* Power spectra of the above */
  int   *np;                    /* Number of points in each */
  float *freqs;                 /* The corresponding frequencies */
  float **W_fft;        /* Fourier transforms of the wavelets for convolution */
  int   *np_fft;                /* Number of points in each the above */
  /*
   * Possibility to add user-defined data
   */
  void             *user_data;      /* Anything else we want */
  mneUserFreeFunc  user_data_free;  /* Function to set the above free */
} *mneWaveletSet,mneWaveletSetRec;
 
typedef struct {                /* Used to store the wavelet transform */
  int   type;                   /* What is stored here? */
  int   nchan;          /* Number of channels */
  int   nsamp;          /* Number of time samples */
  float sfreq;                  /* Sampling frequency */
  float *freqs;         /* Wavelet frequencies */
  int   nfreq;                  /* Number of frequencies */
  float tmin;                   /* Time scale minimum */
  float ***trans;               /* The transforms */
} *mneWaveletTransform,mneWaveletTransformRec;
 
#define MNE_WAVELET_COMPLEX 1
#define MNE_WAVELET_POWER   2
 
/*
 * Environment variables and others
 */
#define MNE_DEFAULT_TRIGGER_CH      "STI 014"
#define MNE_DEFAULT_FILTER_SIZE     4096
#define MNE_ENV_TRIGGER_CH          "MNE_TRIGGER_CH_NAME"
#define MNE_ENV_TRIGGER_CH_MASK     "MNE_TRIGGER_CH_MASK"
#define MNE_ENV_ROOT                "MNE_ROOT"
#define MNE_ENV_FILTER_SIZE         "MNE_FILTER_SIZE"
 
#if defined(__cplusplus) 
}
#endif
#endif