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# help_data_raw

## (Toolbox/help_data_raw.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    helptext = help_data_raw;

### Help Text

    HELP_DATA_RAW - Information on database files of type 'raw'
     function helptext = help_data_raw;

     --------------------- RAW Formats (Binary and ASCII) -------------------------

     The BrainStorm "raw" format is for loading sensor and data from arbitrary
     formats. The file extensions are of keywords {.txt, .raw}. Files of extension
     "txt" are considered ASCII (text) files, and extensions of type "raw" are
     considered as binary files. The formats of each are:

    TXT:
       Each line is terminated with an EOL, each ascii number is separated by white
       space. Data are loaded using Matlab's "load -ascii" convention, see Matlab
       help on "load". Matlab command is load('-ascii',fname). The number of rows
       and columns are automatically inferred from the load routine. In special
       cases, the text file may be a more general string file rather than a simple
       ascii translation of data. See for instance the Channel Labels file.

     RAW:
       All values are written as single precision binary, i.e. four-byte floats.
       See Matlab help on "single" and on "fread". Data are loaded using fread as
       fread(fname,inf,'single'). The first float is the number of rows, the second
       float is the number of columns, and the remaining rows*columns floats are
       the data in the matrix of dimension rows x columns.

     -------------------------- BrainStorm Raw Files ------------------------------

     The result of "load_raw" is a matrix read into matlab. The matrices
       anticipated for loading into BrainStorm are listed and summarized below.

     Channel Location, the Cartesian location of each sensor coil in each channel
     Channel Orientation, the Cartesian orientation of the coil (null for EEG)
     Channel Type, optional text file giving the sensor type (i.e. MEG, EEG, reference)
     Channel Labels, optional text file of names of each sensor (e.g. 'Cz', 'MEG 001')
     Channel Weights, optional file of the reference weights applied in noise
                      cancellation schemes
     Data File, the spatial-temporal or temporal-spatial data matrix
     Data Time, the optional vector of time indices associated with the data

     Details of each file are discussed below

     ---------------------- BrainStorm Raw File Summaries -------------------------

     Channel Location information
       The number of rows is the number of data channels. Each channel is
       characterized by one or more sensors or coils, equal to the number of
       columns x 3 (x, y, z location) in the matrix. Magnetometers have one column,
       1st order gradiometers have two, single-ended EEG have one, differential
       pairs have two. Single-ended EEG also have an additional channel location
       for the reference electrode. Alternatively, enter all EEG channels as two
       columns, the first for the primary electrode, the second for the reference
       electrode. If there is a mix of channel sizes (e.g. magnetometers and
       gradiometers), enter NaN for the additional channels when forming the
       matrix.

       All units are in meters, in Cartestian coordinates with respect to the
       Subject Coordinate System.

     Channel Orientation Information
       In the case of MEG, each coil needs an orientation. The Channel orientation
       matrix is identical in size to the Channel Location matrix. Each three
       elements (cos x, cos y, cos z) is the orientation in Cartesian coordinates
       for the corresponding location. The orientation vector should be unit norm,
       which will be enforced by the import routine. In a mixed sensor type file,
       enter NaN for meaningless orientations. EEG-only can skip this file.

     Optional: Channel Labels
       Optionally, a separate file of channel labels (e.g. 'Cz', 'R12', 'My first
       sensor'), one text line per channel, may be provided. If not provided, then
       default labels of 'MEG Channel 1', etc, will be assigned. Each line of the
       Channel labels file should not be surrounded in quotes.

     Optional: Channel Type
       A raw file may be loaded as all one type (EEG or MEG), but optionally a text
       file may be provided that contains one line per channel, with the following
       keywords (from help_data_channel):
         'MEG', 'EEG', 'MEG REF', 'EEG REG', 'OTHER'
       Each line of the Type file should not be surrounded in quotes

     Optional: Channel Reference Weights
       Noise cancellation schemes generally work by designating some channels as
       "reference", then subtracting the reference channels in a prescribed manner
       from the regular head sensors. For instance, if there are 100 sensors about
       the head and an additional 10 reference sensors in the upper region of the
       Dewar, then the Reference Weights matrix is 100 x 10, giving the
       coefficients necessary to subtract the ten sensors from each channel.

     Optional: Landmark Information
       In addition to the coil locations (both EEG and MEG), "landmarks" or
       "fiducial" points may be entered in an optional file, generally anticipated
       to be points on the scalp. In EEG data, the following fiduciary landmarks
       are necessary in order to establish the subject coordinate system: Nasion,
       Left Pre-aricular, Right Pre-aricular. These landmarks are also explicitly
       found in some MEG data sets. Other landmarks may include the location of
       localizing coils or arbitrary headshape points. The format of the landmark
       file should always be a text file, one line per landmark, in the format '%g
       %g %g %s', where the first three values are the x,y,z Cartesian coordinates
       of the landmark and the last entry is a arbitrary text string. Coordinates
       should be separated spaces, and everything after the third space is taken
       literally as the landmark string, so no quotes should be used,
       example: 0.09 -0.09 0.03 Nasion (PPI measured)

     Data Matrix Information
       The data matrix is nominally a space-time matrix, where each column of the
       matrix represents one time slice, and the number of rows is equal to the
       number of channels. The space-time matrix may be stored as either space-time
       or time-space, as selected by the user at read time. If stored as raw
       (binary), the first two floats should indicate the rows and columns of the
       matrix. If the data are stored as time-space, then after loading the matrix
       will be transposed to space-time. This transposition will cause a noticeable
       delay only in the loading of very large data files. Typically binary data
       are stored "muxed", i.e. by time slice, with the first, say, 151 data points
       equal to the measurements at the 151 sensors in the first time instance. The
       data are loaded as "spatial-temporal."
       By contrast, often ascii data are stored by channel, such that the first
       line of the text file corresponds to the time series for the first sensor.
       These data are loaded as "temporal-spatial", then transposed after loading.
       All Data matrices in BrainStorm are ultimately stored as "spatial-temporal."

       All units should be in MKS, i.e. MEG in Tesla and EEG in Volts.

       The final spatial-temporal (loaded by any above method and transpostion) data
       matrix should have as many rows (channels) as there are channels in the
       Channel matrix. NOTE IN THE CASE OF EEG: For (say) a 128 channel EEG system,
       all single ended, there are actually 129 sensor locations, with the 129th
       (say) the reference electrode. Unlike MEG, there is no recorded 129th
       channel of information, but for bookkeeping purposes in BrainStorm we need a
       virtual 129th channel of data. Either make a channel row of NaN or zero data
       in the data matrix at the same index number as the reference channel
       location, or accept the load routine's request to add such a row.

     Time Vector information
       Since the data may be written in either space-time or time-space, we load
       separately a simple vector of time values, in seconds. For consistency with
       other raw formats, the first two floats should be unity and the length of
       the time series. Text files should just be white space separated text
       numbers, and EOLs will be ignored.

     Reference in the Help Menu: the BrainStorm Document on coordinate Systems.

     See also LOAD_RAW, SAVE_RAW, HELP_DATA_CHANNEL, HELP_DATA_DATA,
              HELP_DATABASE_LIST

### Cross-Reference Information

This function is called by

    bst_static_taskbar                 C:\BrainStorm_2001\Toolbox\bst_static_taskbar.m

### Listing of function C:\BrainStorm_2001\Toolbox\help_data_raw.m

    function helptext = help_data_raw;
    %HELP_DATA_RAW - Information on database files of type 'raw'
    % function helptext = help_data_raw;
    %
    % --------------------- RAW Formats (Binary and ASCII) -------------------------
    %
    % The BrainStorm "raw" format is for loading sensor and data from arbitrary
    % formats. The file extensions are of keywords {.txt, .raw}. Files of extension
    % "txt" are considered ASCII (text) files, and extensions of type "raw" are
    % considered as binary files. The formats of each are:
    %
    %TXT:
    %   Each line is terminated with an EOL, each ascii number is separated by white
    %   space. Data are loaded using Matlab's "load -ascii" convention, see Matlab
    %   help on "load". Matlab command is load('-ascii',fname). The number of rows
    %   and columns are automatically inferred from the load routine. In special
    %   cases, the text file may be a more general string file rather than a simple
    %   ascii translation of data. See for instance the Channel Labels file.
    %
    % RAW:
    %   All values are written as single precision binary, i.e. four-byte floats.
    %   See Matlab help on "single" and on "fread". Data are loaded using fread as
    %   fread(fname,inf,'single'). The first float is the number of rows, the second
    %   float is the number of columns, and the remaining rows*columns floats are
    %   the data in the matrix of dimension rows x columns.
    %
    % -------------------------- BrainStorm Raw Files ------------------------------
    %
    % The result of "load_raw" is a matrix read into matlab. The matrices
    %   anticipated for loading into BrainStorm are listed and summarized below.
    %
    % Channel Location, the Cartesian location of each sensor coil in each channel
    % Channel Orientation, the Cartesian orientation of the coil (null for EEG)
    % Channel Type, optional text file giving the sensor type (i.e. MEG, EEG, reference)
    % Channel Labels, optional text file of names of each sensor (e.g. 'Cz', 'MEG 001')
    % Channel Weights, optional file of the reference weights applied in noise
    %                  cancellation schemes
    % Data File, the spatial-temporal or temporal-spatial data matrix
    % Data Time, the optional vector of time indices associated with the data
    %
    % Details of each file are discussed below
    %
    % ---------------------- BrainStorm Raw File Summaries -------------------------
    %
    % Channel Location information
    %   The number of rows is the number of data channels. Each channel is
    %   characterized by one or more sensors or coils, equal to the number of
    %   columns x 3 (x, y, z location) in the matrix. Magnetometers have one column,
    %   1st order gradiometers have two, single-ended EEG have one, differential
    %   pairs have two. Single-ended EEG also have an additional channel location
    %   for the reference electrode. Alternatively, enter all EEG channels as two
    %   columns, the first for the primary electrode, the second for the reference
    %   electrode. If there is a mix of channel sizes (e.g. magnetometers and
    %   gradiometers), enter NaN for the additional channels when forming the
    %   matrix.
    %
    %   All units are in meters, in Cartestian coordinates with respect to the
    %   Subject Coordinate System.
    %
    % Channel Orientation Information
    %   In the case of MEG, each coil needs an orientation. The Channel orientation
    %   matrix is identical in size to the Channel Location matrix. Each three
    %   elements (cos x, cos y, cos z) is the orientation in Cartesian coordinates
    %   for the corresponding location. The orientation vector should be unit norm,
    %   which will be enforced by the import routine. In a mixed sensor type file,
    %   enter NaN for meaningless orientations. EEG-only can skip this file.
    %
    % Optional: Channel Labels
    %   Optionally, a separate file of channel labels (e.g. 'Cz', 'R12', 'My first
    %   sensor'), one text line per channel, may be provided. If not provided, then
    %   default labels of 'MEG Channel 1', etc, will be assigned. Each line of the
    %   Channel labels file should not be surrounded in quotes.
    %
    % Optional: Channel Type
    %   A raw file may be loaded as all one type (EEG or MEG), but optionally a text
    %   file may be provided that contains one line per channel, with the following
    %   keywords (from help_data_channel):
    %     'MEG', 'EEG', 'MEG REF', 'EEG REG', 'OTHER'
    %   Each line of the Type file should not be surrounded in quotes
    %
    % Optional: Channel Reference Weights
    %   Noise cancellation schemes generally work by designating some channels as
    %   "reference", then subtracting the reference channels in a prescribed manner
    %   from the regular head sensors. For instance, if there are 100 sensors about
    %   the head and an additional 10 reference sensors in the upper region of the
    %   Dewar, then the Reference Weights matrix is 100 x 10, giving the
    %   coefficients necessary to subtract the ten sensors from each channel.
    %
    % Optional: Landmark Information
    %   In addition to the coil locations (both EEG and MEG), "landmarks" or
    %   "fiducial" points may be entered in an optional file, generally anticipated
    %   to be points on the scalp. In EEG data, the following fiduciary landmarks
    %   are necessary in order to establish the subject coordinate system: Nasion,
    %   Left Pre-aricular, Right Pre-aricular. These landmarks are also explicitly
    %   found in some MEG data sets. Other landmarks may include the location of
    %   localizing coils or arbitrary headshape points. The format of the landmark
    %   file should always be a text file, one line per landmark, in the format '%g
    %   %g %g %s', where the first three values are the x,y,z Cartesian coordinates
    %   of the landmark and the last entry is a arbitrary text string. Coordinates
    %   should be separated spaces, and everything after the third space is taken
    %   literally as the landmark string, so no quotes should be used,
    %   example: 0.09 -0.09 0.03 Nasion (PPI measured)
    %
    % Data Matrix Information
    %   The data matrix is nominally a space-time matrix, where each column of the
    %   matrix represents one time slice, and the number of rows is equal to the
    %   number of channels. The space-time matrix may be stored as either space-time
    %   or time-space, as selected by the user at read time. If stored as raw
    %   (binary), the first two floats should indicate the rows and columns of the
    %   matrix. If the data are stored as time-space, then after loading the matrix
    %   will be transposed to space-time. This transposition will cause a noticeable
    %   delay only in the loading of very large data files. Typically binary data
    %   are stored "muxed", i.e. by time slice, with the first, say, 151 data points
    %   equal to the measurements at the 151 sensors in the first time instance. The
    %   data are loaded as "spatial-temporal."
    %   By contrast, often ascii data are stored by channel, such that the first
    %   line of the text file corresponds to the time series for the first sensor.
    %   These data are loaded as "temporal-spatial", then transposed after loading.
    %   All Data matrices in BrainStorm are ultimately stored as "spatial-temporal."
    %
    %   All units should be in MKS, i.e. MEG in Tesla and EEG in Volts.
    %
    %   The final spatial-temporal (loaded by any above method and transpostion) data
    %   matrix should have as many rows (channels) as there are channels in the
    %   Channel matrix. NOTE IN THE CASE OF EEG: For (say) a 128 channel EEG system,
    %   all single ended, there are actually 129 sensor locations, with the 129th
    %   (say) the reference electrode. Unlike MEG, there is no recorded 129th
    %   channel of information, but for bookkeeping purposes in BrainStorm we need a
    %   virtual 129th channel of data. Either make a channel row of NaN or zero data
    %   in the data matrix at the same index number as the reference channel
    %   location, or accept the load routine's request to add such a row.
    %
    % Time Vector information
    %   Since the data may be written in either space-time or time-space, we load
    %   separately a simple vector of time values, in seconds. For consistency with
    %   other raw formats, the first two floats should be unity and the length of
    %   the time series. Text files should just be white space separated text
    %   numbers, and EOLs will be ignored.
    %
    % Reference in the Help Menu: the BrainStorm Document on coordinate Systems.
    %
    % See also LOAD_RAW, SAVE_RAW, HELP_DATA_CHANNEL, HELP_DATA_DATA,
    %          HELP_DATABASE_LIST

    %<autobegin> ---------------------- 26-May-2004 11:30:26 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Help
    %
    % At Check-in: $Author: Mosher $  $Revision: 10 $  $Date: 5/26/04 9:59a $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 24-May-2004
    %
    % Principal Investigators and Developers:
    % ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
    %    University of Southern California, Los Angeles, CA
    % ** John C. Mosher, PhD, Biophysics Group,
    %    Los Alamos National Laboratory, Los Alamos, NM
    % ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
    %    CNRS, Hopital de la Salpetriere, Paris, France
    %
    % See BrainStorm website at http://neuroimage.usc.edu for further information.
    %
    % Copyright (c) 2004 BrainStorm by the University of Southern California
    % This software distributed  under the terms of the GNU General Public License
    % as published by the Free Software Foundation. Further details on the GPL
    % license can be found at http://www.gnu.org/copyleft/gpl.html .
    %
    % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
    % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
    % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
    % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
    % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
    %<autoend> ------------------------ 26-May-2004 11:30:26 -----------------------

    % This help file template was generated by 'make_help' on 16-Apr-2004 10:26:11
    %
    % This help file is callable as "help help_data_raw" (at the command line),
    %  "help_data_raw" (in the Matlab help window), or
    %  "txt = help_data_raw;" (no display, return only txt).

    if nargout,
       helptext = help(mfilename); % return help block to output variable
    else
       helpwin(mfilename); % no output variable, display in help window
    end

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