[Master Index]
[Index for Toolbox]
help_database_list
(Toolbox/help_database_list.m in BrainStorm 2.0 (Alpha))
Function Synopsis
help_database_list;
Help Text
HELP_DATABASE_LIST - Explain the database used by BrainStorm
function help_database_list;
Call as a function or type 'help help_database_list' at the command line
Generate this file using the development tool make_database_list
See the bottom of this help for other links
======================== BRAINSTORM DATABASE LIST ============================
As of 17-Jun-2004 15:59:47
in the Data Root C:\BrainStorm_2001\Phantom
and the Subject Root C:\BrainStorm_2001\Phantom,
the following BrainStorm Database files were identified:
=========================== SUBJECT: FLAG FILE ===============================
These files should match the template '*_brainstormsubject.mat'
Help for this database file (help_data_bstsubject) is given as:
----------------------- Begin help_data_bstsubject ---------------------------
This file is a "flag file" whose presence in a folder indicates that this
folder contains BrainStorm information about a subject (patient).
Anatomy : String name of the MRI data
Comments : String comment about this Subject
DateOfAcquisition : String date for human reference
DateOfModification : String date for human reference
Name : String name of the subject
Tesselation : String name of the tesselation file
Note that Anatomy and Tesselation are no longer used, instead found
separately by searches for *subjectimage* and *tess*
------------------------ End help_data_bstsubject ----------------------------
Mat-files were found matching this type of file.
The fieldnames found in these files were:
Anatomy
Comments
DateOfAcquisition
DateOfModification
Name
Tesselation
The files matching this database type were:
default_subject\sphere_brainstormsubject.mat
montreal_subject\montreal_brainstormsubject.mat
Paris\Paris_brainstormsubject.mat
test_sphere_files\testsphere_brainstormsubject.mat
USC_Skull\PhantomSkull_brainstormsubject.mat
Loading the first mat-file as a structure yields
'sphere_brainstormsubject' has the following fields:
Anatomy: char e.g. 'default_subject\sphere_subjectimage.mat'
Comments: char e.g. 'MRI of a sphere'
DateOfAcquisition: char e.g. '27-May-2004 23:36:33'
DateOfModification: char e.g. '27-May-2004 23:36:33'
Name: char e.g. 'Default Spherical Subject'
Tesselation: empty
===================== SUBJECT: ANATOMICAL INFORMATION ========================
These files should match the template '*image*.mat'
Help for this database file (help_data_image) is given as:
-------------------------- Begin help_data_image -----------------------------
Cube : is the actual image set, x, y, z, left to right, back to front,
bottom to top, of size M x N x P.
DataClass : a string describing the bit encoding of the gray levels (e.g. 'ushort')
Voxsize : Size of a voxel in mm (e.g. [0.9375 0.9375 0.9375])
scantype : a string label indicating the scan direction (e.g. 'Axial')
SCS : structure with fields:
FiducialName : cell array of ORDERED fiducial labels,
nasion, left and right and origin)
(e.g. 'Nasion', 'Left ear','Right ear', 'CTF Origin')
(additional fiducials are stored in Landmarks below).
mmCubeFiducial : is 3 x n array of ORDERED coordinate fiducial points
in mm (see FiducialName)
MRI coordinates relative to 0,0,0 point.
System : keyword, {'CTF','NEUROMAG'}
R : 3x3 rotation matrix (cosines)
T : translation 3x1 vector (units of mm)
Transformation formulas are:
x(SCS coordinates) = R * x(MRI coordinates) + T
x(MRI) = inv(R)*(x(SCS) - T)
Landmarks : a structure specifying locations of extra points of interests with fields:
MRImmXYZ : a 3xn array of landmark locations in mm and MRI coordinate system
Names : a cell array of string used to label the landmarks
See http://neuroimage.usc.edu/brainstorm/GUI_CoordinateSystem.htm
--------------------------- End help_data_image ------------------------------
Mat-files were found matching this type of file.
The fieldnames found in these files were:
Comment
Cube
DataClase
DataClass
Landmarks
PCS
SCS
Segment
Voxsize
filename
scantype
The files matching this database type were:
default_subject\sphere_subjectimage.mat
**(missing fields: Comment PCS Segment filename)
montreal_subject\montreal_subjectimage.mat
**(missing fields: Comment DataClase PCS Segment filename)
test_sphere_files\subjectimage.mat
**(missing fields: DataClase DataClass Landmarks)
test_sphere_files\subjectimage2.mat
**(missing fields: Comment DataClase DataClass Landmarks PCS filename)
Loading the first mat-file as a structure yields
'sphere_subjectimage' has the following fields:
Cube: uint8
DataClase: char e.g. 'uint8'
DataClass: empty
Landmarks: [1x1 struct]
SCS: [1x1 struct]
Voxsize: [1x3 double]
scantype: char e.g. 'Axial'
Structure 'Landmarks' has the following fields:
MRImmXYZ: [3x2 double]
Names: [1x2 cell]
Structure 'SCS' has the following fields:
FiducialName: [1x4 cell]
R: [3x3 double]
System: char e.g. 'CTF'
T: [3x1 double]
mmCubeFiducial: [3x4 double]
==================== SUBJECT: TESSELATION INFORMATION ========================
These files should match the template '*tess*.mat'
Help for this database file (help_data_tess) is given as:
-------------------------- Begin help_data_tess ------------------------------
Comment : Cell array, each element a descriptive string
Faces : Cell array, each element a m x 3 matrix of m face descriptors
Vertices : Cell array, each element a 3 x n matrix of the n vertex
positions in Cartesian coordinates
Note that Vertices is the transpose (3 x n) of what is expected in the "patch"
command (n x 3) and generally other tessellation routines.
The ordering of the faces vertices must be such that 1 - 2 - 3 points
"outward" by the right-hand rule. The outward orientation of the triangle is
important for good visualization lighting, but it is critical for the proper
calculation of boundary elements.
--------------------------- End help_data_tess -------------------------------
Mat-files were found matching this type of file.
The fieldnames found in these files were:
Clusters
Comment
Curvature
Faces
VertConn
Vertices
The files matching this database type were:
montreal_subject\montreal_3layer_tess.mat
**(missing fields: Clusters Curvature VertConn)
montreal_subject\montreal_white_matter_tess.mat
**(missing fields: Clusters)
Paris\paradis_tess-CTF.mat
Paris\para_brain-CTF_tess.mat
**(missing fields: Clusters Curvature VertConn)
Paris\para_brain-CTF_tess_alignedCTF.mat
**(missing fields: Clusters Curvature VertConn)
Paris\para_head-CTF_tess.mat
**(missing fields: Clusters Curvature VertConn)
Paris\para_head-CTF_tess_alignedCTF.mat
**(missing fields: Clusters Curvature VertConn)
test_sphere_files\subjecttess.mat
**(missing fields: Clusters Curvature VertConn)
USC_Skull\cortex_subjecttess.mat
**(missing fields: Clusters)
USC_Skull\scalp_subjecttess.mat
**(missing fields: Clusters Curvature VertConn)
USC_Skull\skull_subjecttess.mat
**(missing fields: Clusters Curvature VertConn)
USC_Skull\subjecttess_vertconn.mat
**(missing fields: Clusters Comment Curvature Faces Vertices)
Loading the first mat-file as a structure yields
'montreal_3layer_tess' has the following fields:
Comment: [1x3 cell]
Faces: [3x1 cell]
Vertices: [3x1 cell]
================= SUBJECT: TESSELATION FACES CONNECTIVITY ====================
These files should match the template '*triconn*.mat'
Help for this database file (help_data_triconn) is given as:
------------------------- Begin help_data_triconn ----------------------------
(add help information)
-------------------------- End help_data_triconn -----------------------------
No such files found in the database
=============== SUBJECT: TESSELATION VERTICES CONNECTIVITY ===================
These files should match the template '*vertconn*.mat'
Help for this database file (help_data_vertconn) is given as:
------------------------ Begin help_data_vertconn ----------------------------
(add help information)
------------------------- End help_data_vertconn -----------------------------
Mat-files were found matching this type of file.
The fieldnames found in these files were:
VertConn
The files matching this database type were:
USC_Skull\subjecttess_vertconn.mat
Loading the first mat-file as a structure yields
'subjecttess_vertconn' has the following fields:
VertConn: [4x1 cell]
========================== STUDY: DATA FLAG FILE =============================
These files should match the template '*_brainstormstudy.mat'
Help for this database file (help_data_bststudy) is given as:
------------------------ Begin help_data_bststudy ----------------------------
The presence of this file in a folder signals BrainStorm that the folder
contains data and associated files for analysis.
BrainStormSubject: String referential filename to the _brainstormsubject.mat
DateOfModification: String human reference '18-Sep-2003 09:35:20'
DateOfStudy: String human reference '18-Sep-2003 09:35:20'
Name: String human reference 'John Doe'
Session: String human reference 'Simulated Sphere Data'
------------------------- End help_data_bststudy -----------------------------
Mat-files were found matching this type of file.
The fieldnames found in these files were:
BrainStormSubject
DateOfModification
DateOfStudy
Name
Session
Subject
append
The files matching this database type were:
default_data\sphere_brainstormstudy.mat
**(missing fields: Subject)
jlh_test\JLH_brainstormstudy.mat
**(missing fields: Subject)
montreal_data\montreal_brainstormstudy.mat
**(missing fields: Subject)
Sample_Raw\Mixed_brainstormstudy.mat
**(missing fields: Subject)
simulated\sphere_brainstormstudy.mat
**(missing fields: append)
test_sphere_files\testsphere_brainstormstudy.mat
**(missing fields: Subject)
Loading the first mat-file as a structure yields
'sphere_brainstormstudy' has the following fields:
BrainStormSubject: char e.g. 'montreal_subject\montreal_brainstormsubject.mat'
DateOfModification: char e.g. '27-May-2004 23:36:34'
DateOfStudy: char e.g. '27-May-2004 23:36:34'
Name: char e.g. 'Sample Raw'
Session: char e.g. 'Simulated Sphere Data'
append: char e.g. '-append'
==================== STUDY: SENSOR CHANNEL INFORMATION =======================
These files should match the template '*channel*.mat'
Help for this database file (help_data_channel) is given as:
------------------------- Begin help_data_channel ----------------------------
Landmark : a structure specifying locations of extra points of interests with fields:
Loc : a 3 x n array of landmark locations in meters coordinate system
Name : a 1 x n cell array of string used to label the landmarks
Channel : An array of structures. Each element in the array comprises
the following fields
Loc : 3 x n, one column per coil, location in meters in SCS
Weight : 1 x n, relative gradiometer weights, e.g. [1 -1] or [1 -2 1]
Orient : 3 x n, one column per coil, Cartesian orientation in SCS
Type : String, must be {'MEG', 'EEG', 'MEG REF','EEG REF', 'OTHER'};
Name : String, short label, usually machine assigned 'MEG 001'
Comment : See explanation below
The Comment field is somewhat complicated, CBB.
Comment : Keywords or data. If TYPE is 'EEG' and data are average referenced,
then Comment must be 'AVERAGE REF', and all Loc are a single location.
If EEG are data are differential, then two Loc and Weights
are used, and Comment is '' (blank).
If EEG data are single ended, then Loc is one location,
there can ONLY be one Type of 'EEG REF', Comment is '', and
algorithms know to search for the reference channel.
If MEG data, and there are reference channels, the
reference channels are marked Type 'MEG REF'. Then the
FIRST Channel of Type 'MEG' has a Comment field that gives
the transformation matrix that builds the higher
gradiometers. See notes below for calculation method.
Obsolete
System : String e.g. 'CTF 151', this field apparently not used.
-- Notes --
SCS is the patient coordinate system, i.e. the coil location is with respect
to the subject's origin. See BrainStorm reference on coordinate systems:
http://neuroimage.usc.edu/brainstorm/GUI_CoordinateSystem.htm
A "channel" comprises the locations of the array's output, usually the
result of combining "n" different coil locations.
The reference channels are used to form "virtual gradiometers." If there are
151 head channels (Type 'MEG') and 29 reference channels (Type 'MEG REF'),
then the reference weighting matrix is 151 x 29. The 151 originally recorded
data channels are modified in the machine or external to BrainStorm as Ffinal
= Forg - W*Fref; If Gfinal is the gain matrix for the noise-weighted gain
matrix (151 rows), Ghead is the gain matrix for each channel without noise
weighting (151 rows), Gref is the gain matrix for each of the reference
channels (29 rows), and W is the reference channel weights, then:
Gfinal = Ghead - W*Gref;
See help_data_raw for descriptions on how to manually store this information
and importation. At this time, CTF weighting information is automatically
handled.
-------------------------- End help_data_channel -----------------------------
Mat-files were found matching this type of file.
The fieldnames found in these files were:
Channel
The files matching this database type were:
default_data\sphere_channel.mat
jlh_test\JLH_channel.mat
montreal_data\montreal_channel.mat
Sample_Raw\Mixed_channel.mat
simulated\sphere_channel.mat
test_sphere_files\testsphere_channels.mat
USC_Skull\EEG_channel.mat
Loading the first mat-file as a structure yields
'sphere_channel' has the following fields:
Channel: [1x138 struct]
Structure 'Channel' has the following fields:
Comment: char e.g. 'Simulated magnetometer #001'
Loc: [3x1 double]
Name: char e.g. 'MEG 001'
Orient: [3x1 double]
System: char e.g. 'ctf'
Type: char e.g. 'MEG'
Weight: [1x1 double] e.g. 1
============= STUDY: FORWARD PROBLEM (HEAD AND SENSOR) MODEL =================
These files should match the template '*headmodel*.mat'
Help for this database file (help_data_headmodel) is given as:
------------------------ Begin help_data_headmodel ---------------------------
For m channels of data:
Gain : [1x1 cell]
GridLoc : [1x1 cell]
GridName : [1x1 cell]
HeadModelName : char e.g. 'meg_sphere'
HeadModelType : char e.g. 'SearchGrid'
MEGMethod : char e.g. 'meg_sphere'
Param : [1x138 struct]
SourceOrder : [1x1 double] e.g. -1
Structure 'Param' has the following fields:
Berg : empty
Center : [3x1 double]
Conductivity : empty
EEGType : empty
Order : [1x1 double] e.g. -1
Radii : [1x3 double]
------------------------- End help_data_headmodel ----------------------------
Mat-files were found matching this type of file.
The fieldnames found in these files were:
EEGMethod
Function
Gain
GainCovar
GainCovarName
GainCovar_ColNorm
GridLoc
GridName
GridOrient
HeadModelName
HeadModelType
MEGMethod
Param
SourceOrder
iGrid
The files matching this database type were:
default_data\sphere_headmodelVolGrid_CD.mat
**(missing fields: EEGMethod GainCovar GainCovarName GainCovar_ColNorm GridOrient iGrid)
jlh_test\JLH_headmodelVolGrid_CD.mat
**(missing fields: GainCovar GainCovarName GainCovar_ColNorm GridOrient MEGMethod iGrid)
montreal_data\montreal_headmodelSurfGrid_CD.mat
**(missing fields: EEGMethod)
montreal_data\montreal_headmodelVolGrid_CD.mat
**(missing fields: EEGMethod GainCovar GainCovarName GainCovar_ColNorm GridOrient iGrid)
test_sphere_files\testsphere_headmodelVolGrid_CD.mat
**(missing fields: EEGMethod GainCovar GainCovarName GainCovar_ColNorm GridOrient iGrid)
test_sphere_files\testsphere_headmodelVolGrid_CD_1.mat
**(missing fields: EEGMethod GainCovar GainCovarName GainCovar_ColNorm GridOrient iGrid)
Loading the first mat-file as a structure yields
'sphere_headmodelVolGrid_CD' has the following fields:
Function: [1x138 cell]
Gain: [1x1 cell]
GridLoc: [1x1 cell]
GridName: [1x1 cell]
HeadModelName: char e.g. 'meg_sphere'
HeadModelType: char e.g. 'SearchGrid'
MEGMethod: char e.g. 'meg_sphere'
Param: [1x138 struct]
SourceOrder: [1x1 double] e.g. -1
Structure 'Param' has the following fields:
Berg: empty
Center: [3x1 double]
Conductivity: empty
EEGType: empty
Order: [1x1 double] e.g. -1
Radii: [1x3 double]
========================= STUDY: EEG OR MEG DATA =============================
These files should match the template '*data*.mat'
Help for this database file (help_data_data) is given as:
-------------------------- Begin help_data_data ------------------------------
For m channels of data over n samples of time:
ChannelFlag : 1 x length(Channel) of {0,1} to indicate whether or not to use
Warning: when data is measured w.r.t. some reference channel(s),
ChannelFlag and F (see below) are of length of Channel.
Channel being the Channel structure stored in a companion
channel*.mat file in the same fodler as the *data*.mat file.
Comment : String for human reference 'Simulated Data'
Device : String information words e.g. 'Neuromag', 'CTF',
deprecated by still in use by information displays.
System : String, key words {'CTF','NEUROMAG'};
Establishes the coordinate system used
F : The Spatio-temporal length(Channel) x n data matrix in
MKS units (Telsa, Volt)
NoiseCov : Sqrt of the noise covariance matrix, m x m (all channels),
in development
Projector : empty, in development
SourceCov : empty, in development
Time : 1 x n of time indices in seconds
--------------------------- End help_data_data -------------------------------
Mat-files were found matching this type of file.
The fieldnames found in these files were:
ChannelFlag
Comment
Device
F
NoiseCov
Project
Projector
SourceCov
System
Time
The files matching this database type were:
default_data\sphere_data_363398.mat
**(missing fields: Project System)
jlh_test\JLH_data.mat
**(missing fields: Project)
montreal_data\montreal_data_4713.mat
**(missing fields: Project)
Sample_Raw\Mixed_data.mat
**(missing fields: Project)
simulated\sphere_data_054333.mat
**(missing fields: Project System)
test_sphere_files\testsphere_data.mat
**(missing fields: System)
USC_Skull\EEG_data6.mat
**(missing fields: Project)
Loading the first mat-file as a structure yields
'sphere_data_363398' has the following fields:
ChannelFlag: [1x138 double]
Comment: char e.g. 'Simulated Data'
Device: char e.g. 'Ctf_Axial'
F: [138x100 double]
NoiseCov: empty
Projector: empty
SourceCov: empty
Time: [1x100 double]
===================== STUDY: INVERSE PROBLEM RESULTS =========================
These files should match the template '*results*.mat'
Help for this database file (help_data_results) is given as:
------------------------- Begin help_data_results ----------------------------
Center: [3x1 double]
Comment: char e.g. 'Simulated data'
DataFlag : a string specifiying the type of data the results originate from
'MEG', 'EEG', 'Fusion'
Fsynth: [138x100 double]
IndepTopo: [138x3 double]
SourceLoc: [1x3 cell]
SourceOrientation: [1x3 cell]
Time: [1x100 double]
TimeSeries: [100x3 double]
-------------------------- End help_data_results -----------------------------
Mat-files were found matching this type of file.
The fieldnames found in these files were:
Center
Channel
ChannelFlag
Comment
DataFile
DataFlag
Date
Fsynth
Function
GUI
HeadModelFile
ImageGridAmp
ImageGridTime
ImagingKernel
IndepTopo
ModelGain
NoiseCov
OPTIONS
PatchAmp
PatchNdx
Projector
Residuals
SourceCorrelation
SourceCov
SourceLoc
SourceOrder
SourceOrientation
Study
StudySubject
Subject
Time
TimeSeries
The files matching this database type were:
default_data\sphere_results_363398.mat
**(missing fields: Channel ChannelFlag DataFile DataFlag Date Function GUI HeadModelFile ImageGridAmp ImageGridTime ImagingKernel ModelGain NoiseCov OPTIONS PatchAmp PatchNdx Projector Residuals SourceCorrelation SourceCov SourceOrder Study StudySubject Subject)
default_data\sphere_results_363398_1530.mat
**(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
jlh_test\JLH_results_1011.mat
**(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
jlh_test\JLH_results_1154.mat
**(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
jlh_test\JLH_results_1534.mat
**(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
jlh_test\JLH_results_1536.mat
**(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
jlh_test\JLH_results_1629.mat
**(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
montreal_data\montreal_results_4713_1548.mat
**(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
montreal_data\montreal_results_4713_MNE_MEG_1550.mat
**(missing fields: Center DataFlag GUI IndepTopo SourceCorrelation Study StudySubject Subject)
simulated\sphere_results_054333.mat
**(missing fields: Channel ChannelFlag DataFile DataFlag Date Function GUI HeadModelFile ImageGridAmp ImageGridTime ImagingKernel ModelGain NoiseCov OPTIONS PatchAmp PatchNdx Projector Residuals SourceCorrelation SourceCov SourceOrder Study StudySubject Subject)
test_sphere_files\testsphere_results_1349.mat
**(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
Loading the first mat-file as a structure yields
'sphere_results_363398' has the following fields:
Center: [3x1 double]
Comment: char e.g. 'Simulated data'
Fsynth: [138x100 double]
IndepTopo: [138x3 double]
SourceLoc: [1x3 cell]
SourceOrientation: [1x3 cell]
Time: [1x100 double]
TimeSeries: [100x3 double]
See also HELP_DATA_BSTSUBJECT, HELP_DATA_IMAGE, HELP_DATA_TESS
HELP_DATA_TRICONN, HELP_DATA_VERTCONN, HELP_DATA_BSTSTUDY
HELP_DATA_CHANNEL, HELP_DATA_HEADMODEL, HELP_DATA_DATA
HELP_DATA_RESULTS
Cross-Reference Information
This function is called by
Listing of function C:\BrainStorm_2001\Toolbox\help_database_list.m
function help_database_list;
%HELP_DATABASE_LIST - Explain the database used by BrainStorm
% function help_database_list;
% Call as a function or type 'help help_database_list' at the command line
%
% Generate this file using the development tool make_database_list
%
% See the bottom of this help for other links
%
% ======================== BRAINSTORM DATABASE LIST ============================
%
% As of 17-Jun-2004 15:59:47
% in the Data Root C:\BrainStorm_2001\Phantom
% and the Subject Root C:\BrainStorm_2001\Phantom,
%
% the following BrainStorm Database files were identified:
%
%
%
% =========================== SUBJECT: FLAG FILE ===============================
%
% These files should match the template '*_brainstormsubject.mat'
%
% Help for this database file (help_data_bstsubject) is given as:
%
% ----------------------- Begin help_data_bstsubject ---------------------------
% This file is a "flag file" whose presence in a folder indicates that this
% folder contains BrainStorm information about a subject (patient).
%
% Anatomy : String name of the MRI data
% Comments : String comment about this Subject
% DateOfAcquisition : String date for human reference
% DateOfModification : String date for human reference
% Name : String name of the subject
% Tesselation : String name of the tesselation file
%
% Note that Anatomy and Tesselation are no longer used, instead found
% separately by searches for *subjectimage* and *tess*
% ------------------------ End help_data_bstsubject ----------------------------
%
% Mat-files were found matching this type of file.
% The fieldnames found in these files were:
%
% Anatomy
% Comments
% DateOfAcquisition
% DateOfModification
% Name
% Tesselation
%
% The files matching this database type were:
%
% default_subject\sphere_brainstormsubject.mat
% montreal_subject\montreal_brainstormsubject.mat
% Paris\Paris_brainstormsubject.mat
% test_sphere_files\testsphere_brainstormsubject.mat
% USC_Skull\PhantomSkull_brainstormsubject.mat
%
% Loading the first mat-file as a structure yields
%
% 'sphere_brainstormsubject' has the following fields:
% Anatomy: char e.g. 'default_subject\sphere_subjectimage.mat'
% Comments: char e.g. 'MRI of a sphere'
% DateOfAcquisition: char e.g. '27-May-2004 23:36:33'
% DateOfModification: char e.g. '27-May-2004 23:36:33'
% Name: char e.g. 'Default Spherical Subject'
% Tesselation: empty
%
%
%
% ===================== SUBJECT: ANATOMICAL INFORMATION ========================
%
% These files should match the template '*image*.mat'
%
% Help for this database file (help_data_image) is given as:
%
% -------------------------- Begin help_data_image -----------------------------
%
% Cube : is the actual image set, x, y, z, left to right, back to front,
% bottom to top, of size M x N x P.
% DataClass : a string describing the bit encoding of the gray levels (e.g. 'ushort')
% Voxsize : Size of a voxel in mm (e.g. [0.9375 0.9375 0.9375])
% scantype : a string label indicating the scan direction (e.g. 'Axial')
% SCS : structure with fields:
% FiducialName : cell array of ORDERED fiducial labels,
% nasion, left and right and origin)
% (e.g. 'Nasion', 'Left ear','Right ear', 'CTF Origin')
% (additional fiducials are stored in Landmarks below).
% mmCubeFiducial : is 3 x n array of ORDERED coordinate fiducial points
% in mm (see FiducialName)
% MRI coordinates relative to 0,0,0 point.
% System : keyword, {'CTF','NEUROMAG'}
% R : 3x3 rotation matrix (cosines)
% T : translation 3x1 vector (units of mm)
%
% Transformation formulas are:
% x(SCS coordinates) = R * x(MRI coordinates) + T
% x(MRI) = inv(R)*(x(SCS) - T)
%
% Landmarks : a structure specifying locations of extra points of interests with fields:
% MRImmXYZ : a 3xn array of landmark locations in mm and MRI coordinate system
% Names : a cell array of string used to label the landmarks
%
% See http://neuroimage.usc.edu/brainstorm/GUI_CoordinateSystem.htm
%
% --------------------------- End help_data_image ------------------------------
%
% Mat-files were found matching this type of file.
% The fieldnames found in these files were:
%
% Comment
% Cube
% DataClase
% DataClass
% Landmarks
% PCS
% SCS
% Segment
% Voxsize
% filename
% scantype
%
% The files matching this database type were:
%
% default_subject\sphere_subjectimage.mat
% **(missing fields: Comment PCS Segment filename)
% montreal_subject\montreal_subjectimage.mat
% **(missing fields: Comment DataClase PCS Segment filename)
% test_sphere_files\subjectimage.mat
% **(missing fields: DataClase DataClass Landmarks)
% test_sphere_files\subjectimage2.mat
% **(missing fields: Comment DataClase DataClass Landmarks PCS filename)
%
% Loading the first mat-file as a structure yields
%
% 'sphere_subjectimage' has the following fields:
% Cube: uint8
% DataClase: char e.g. 'uint8'
% DataClass: empty
% Landmarks: [1x1 struct]
% SCS: [1x1 struct]
% Voxsize: [1x3 double]
% scantype: char e.g. 'Axial'
%
% Structure 'Landmarks' has the following fields:
% MRImmXYZ: [3x2 double]
% Names: [1x2 cell]
%
% Structure 'SCS' has the following fields:
% FiducialName: [1x4 cell]
% R: [3x3 double]
% System: char e.g. 'CTF'
% T: [3x1 double]
% mmCubeFiducial: [3x4 double]
%
%
%
% ==================== SUBJECT: TESSELATION INFORMATION ========================
%
% These files should match the template '*tess*.mat'
%
% Help for this database file (help_data_tess) is given as:
%
% -------------------------- Begin help_data_tess ------------------------------
% Comment : Cell array, each element a descriptive string
% Faces : Cell array, each element a m x 3 matrix of m face descriptors
% Vertices : Cell array, each element a 3 x n matrix of the n vertex
% positions in Cartesian coordinates
%
% Note that Vertices is the transpose (3 x n) of what is expected in the "patch"
% command (n x 3) and generally other tessellation routines.
%
% The ordering of the faces vertices must be such that 1 - 2 - 3 points
% "outward" by the right-hand rule. The outward orientation of the triangle is
% important for good visualization lighting, but it is critical for the proper
% calculation of boundary elements.
% --------------------------- End help_data_tess -------------------------------
%
% Mat-files were found matching this type of file.
% The fieldnames found in these files were:
%
% Clusters
% Comment
% Curvature
% Faces
% VertConn
% Vertices
%
% The files matching this database type were:
%
% montreal_subject\montreal_3layer_tess.mat
% **(missing fields: Clusters Curvature VertConn)
% montreal_subject\montreal_white_matter_tess.mat
% **(missing fields: Clusters)
% Paris\paradis_tess-CTF.mat
% Paris\para_brain-CTF_tess.mat
% **(missing fields: Clusters Curvature VertConn)
% Paris\para_brain-CTF_tess_alignedCTF.mat
% **(missing fields: Clusters Curvature VertConn)
% Paris\para_head-CTF_tess.mat
% **(missing fields: Clusters Curvature VertConn)
% Paris\para_head-CTF_tess_alignedCTF.mat
% **(missing fields: Clusters Curvature VertConn)
% test_sphere_files\subjecttess.mat
% **(missing fields: Clusters Curvature VertConn)
% USC_Skull\cortex_subjecttess.mat
% **(missing fields: Clusters)
% USC_Skull\scalp_subjecttess.mat
% **(missing fields: Clusters Curvature VertConn)
% USC_Skull\skull_subjecttess.mat
% **(missing fields: Clusters Curvature VertConn)
% USC_Skull\subjecttess_vertconn.mat
% **(missing fields: Clusters Comment Curvature Faces Vertices)
%
% Loading the first mat-file as a structure yields
%
% 'montreal_3layer_tess' has the following fields:
% Comment: [1x3 cell]
% Faces: [3x1 cell]
% Vertices: [3x1 cell]
%
%
%
% ================= SUBJECT: TESSELATION FACES CONNECTIVITY ====================
%
% These files should match the template '*triconn*.mat'
%
% Help for this database file (help_data_triconn) is given as:
%
% ------------------------- Begin help_data_triconn ----------------------------
% (add help information)
% -------------------------- End help_data_triconn -----------------------------
%
% No such files found in the database
%
%
%
% =============== SUBJECT: TESSELATION VERTICES CONNECTIVITY ===================
%
% These files should match the template '*vertconn*.mat'
%
% Help for this database file (help_data_vertconn) is given as:
%
% ------------------------ Begin help_data_vertconn ----------------------------
% (add help information)
% ------------------------- End help_data_vertconn -----------------------------
%
% Mat-files were found matching this type of file.
% The fieldnames found in these files were:
%
% VertConn
%
% The files matching this database type were:
%
% USC_Skull\subjecttess_vertconn.mat
%
% Loading the first mat-file as a structure yields
%
% 'subjecttess_vertconn' has the following fields:
% VertConn: [4x1 cell]
%
%
%
% ========================== STUDY: DATA FLAG FILE =============================
%
% These files should match the template '*_brainstormstudy.mat'
%
% Help for this database file (help_data_bststudy) is given as:
%
% ------------------------ Begin help_data_bststudy ----------------------------
% The presence of this file in a folder signals BrainStorm that the folder
% contains data and associated files for analysis.
%
% BrainStormSubject: String referential filename to the _brainstormsubject.mat
% DateOfModification: String human reference '18-Sep-2003 09:35:20'
% DateOfStudy: String human reference '18-Sep-2003 09:35:20'
% Name: String human reference 'John Doe'
% Session: String human reference 'Simulated Sphere Data'
% ------------------------- End help_data_bststudy -----------------------------
%
% Mat-files were found matching this type of file.
% The fieldnames found in these files were:
%
% BrainStormSubject
% DateOfModification
% DateOfStudy
% Name
% Session
% Subject
% append
%
% The files matching this database type were:
%
% default_data\sphere_brainstormstudy.mat
% **(missing fields: Subject)
% jlh_test\JLH_brainstormstudy.mat
% **(missing fields: Subject)
% montreal_data\montreal_brainstormstudy.mat
% **(missing fields: Subject)
% Sample_Raw\Mixed_brainstormstudy.mat
% **(missing fields: Subject)
% simulated\sphere_brainstormstudy.mat
% **(missing fields: append)
% test_sphere_files\testsphere_brainstormstudy.mat
% **(missing fields: Subject)
%
% Loading the first mat-file as a structure yields
%
% 'sphere_brainstormstudy' has the following fields:
% BrainStormSubject: char e.g. 'montreal_subject\montreal_brainstormsubject.mat'
% DateOfModification: char e.g. '27-May-2004 23:36:34'
% DateOfStudy: char e.g. '27-May-2004 23:36:34'
% Name: char e.g. 'Sample Raw'
% Session: char e.g. 'Simulated Sphere Data'
% append: char e.g. '-append'
%
%
%
% ==================== STUDY: SENSOR CHANNEL INFORMATION =======================
%
% These files should match the template '*channel*.mat'
%
% Help for this database file (help_data_channel) is given as:
%
% ------------------------- Begin help_data_channel ----------------------------
%
% Landmark : a structure specifying locations of extra points of interests with fields:
% Loc : a 3 x n array of landmark locations in meters coordinate system
% Name : a 1 x n cell array of string used to label the landmarks
%
% Channel : An array of structures. Each element in the array comprises
% the following fields
% Loc : 3 x n, one column per coil, location in meters in SCS
% Weight : 1 x n, relative gradiometer weights, e.g. [1 -1] or [1 -2 1]
% Orient : 3 x n, one column per coil, Cartesian orientation in SCS
% Type : String, must be {'MEG', 'EEG', 'MEG REF','EEG REF', 'OTHER'};
% Name : String, short label, usually machine assigned 'MEG 001'
% Comment : See explanation below
%
% The Comment field is somewhat complicated, CBB.
% Comment : Keywords or data. If TYPE is 'EEG' and data are average referenced,
% then Comment must be 'AVERAGE REF', and all Loc are a single location.
% If EEG are data are differential, then two Loc and Weights
% are used, and Comment is '' (blank).
% If EEG data are single ended, then Loc is one location,
% there can ONLY be one Type of 'EEG REF', Comment is '', and
% algorithms know to search for the reference channel.
% If MEG data, and there are reference channels, the
% reference channels are marked Type 'MEG REF'. Then the
% FIRST Channel of Type 'MEG' has a Comment field that gives
% the transformation matrix that builds the higher
% gradiometers. See notes below for calculation method.
%
% Obsolete
% System : String e.g. 'CTF 151', this field apparently not used.
%
% -- Notes --
% SCS is the patient coordinate system, i.e. the coil location is with respect
% to the subject's origin. See BrainStorm reference on coordinate systems:
%
% http://neuroimage.usc.edu/brainstorm/GUI_CoordinateSystem.htm
%
% A "channel" comprises the locations of the array's output, usually the
% result of combining "n" different coil locations.
%
% The reference channels are used to form "virtual gradiometers." If there are
% 151 head channels (Type 'MEG') and 29 reference channels (Type 'MEG REF'),
% then the reference weighting matrix is 151 x 29. The 151 originally recorded
% data channels are modified in the machine or external to BrainStorm as Ffinal
% = Forg - W*Fref; If Gfinal is the gain matrix for the noise-weighted gain
% matrix (151 rows), Ghead is the gain matrix for each channel without noise
% weighting (151 rows), Gref is the gain matrix for each of the reference
% channels (29 rows), and W is the reference channel weights, then:
%
% Gfinal = Ghead - W*Gref;
%
% See help_data_raw for descriptions on how to manually store this information
% and importation. At this time, CTF weighting information is automatically
% handled.
%
% -------------------------- End help_data_channel -----------------------------
%
% Mat-files were found matching this type of file.
% The fieldnames found in these files were:
%
% Channel
%
% The files matching this database type were:
%
% default_data\sphere_channel.mat
% jlh_test\JLH_channel.mat
% montreal_data\montreal_channel.mat
% Sample_Raw\Mixed_channel.mat
% simulated\sphere_channel.mat
% test_sphere_files\testsphere_channels.mat
% USC_Skull\EEG_channel.mat
%
% Loading the first mat-file as a structure yields
%
% 'sphere_channel' has the following fields:
% Channel: [1x138 struct]
%
% Structure 'Channel' has the following fields:
% Comment: char e.g. 'Simulated magnetometer #001'
% Loc: [3x1 double]
% Name: char e.g. 'MEG 001'
% Orient: [3x1 double]
% System: char e.g. 'ctf'
% Type: char e.g. 'MEG'
% Weight: [1x1 double] e.g. 1
%
%
%
% ============= STUDY: FORWARD PROBLEM (HEAD AND SENSOR) MODEL =================
%
% These files should match the template '*headmodel*.mat'
%
% Help for this database file (help_data_headmodel) is given as:
%
% ------------------------ Begin help_data_headmodel ---------------------------
% For m channels of data:
% Gain : [1x1 cell]
% GridLoc : [1x1 cell]
% GridName : [1x1 cell]
% HeadModelName : char e.g. 'meg_sphere'
% HeadModelType : char e.g. 'SearchGrid'
% MEGMethod : char e.g. 'meg_sphere'
% Param : [1x138 struct]
% SourceOrder : [1x1 double] e.g. -1
%
% Structure 'Param' has the following fields:
% Berg : empty
% Center : [3x1 double]
% Conductivity : empty
% EEGType : empty
% Order : [1x1 double] e.g. -1
% Radii : [1x3 double]
% ------------------------- End help_data_headmodel ----------------------------
%
% Mat-files were found matching this type of file.
% The fieldnames found in these files were:
%
% EEGMethod
% Function
% Gain
% GainCovar
% GainCovarName
% GainCovar_ColNorm
% GridLoc
% GridName
% GridOrient
% HeadModelName
% HeadModelType
% MEGMethod
% Param
% SourceOrder
% iGrid
%
% The files matching this database type were:
%
% default_data\sphere_headmodelVolGrid_CD.mat
% **(missing fields: EEGMethod GainCovar GainCovarName GainCovar_ColNorm GridOrient iGrid)
% jlh_test\JLH_headmodelVolGrid_CD.mat
% **(missing fields: GainCovar GainCovarName GainCovar_ColNorm GridOrient MEGMethod iGrid)
% montreal_data\montreal_headmodelSurfGrid_CD.mat
% **(missing fields: EEGMethod)
% montreal_data\montreal_headmodelVolGrid_CD.mat
% **(missing fields: EEGMethod GainCovar GainCovarName GainCovar_ColNorm GridOrient iGrid)
% test_sphere_files\testsphere_headmodelVolGrid_CD.mat
% **(missing fields: EEGMethod GainCovar GainCovarName GainCovar_ColNorm GridOrient iGrid)
% test_sphere_files\testsphere_headmodelVolGrid_CD_1.mat
% **(missing fields: EEGMethod GainCovar GainCovarName GainCovar_ColNorm GridOrient iGrid)
%
% Loading the first mat-file as a structure yields
%
% 'sphere_headmodelVolGrid_CD' has the following fields:
% Function: [1x138 cell]
% Gain: [1x1 cell]
% GridLoc: [1x1 cell]
% GridName: [1x1 cell]
% HeadModelName: char e.g. 'meg_sphere'
% HeadModelType: char e.g. 'SearchGrid'
% MEGMethod: char e.g. 'meg_sphere'
% Param: [1x138 struct]
% SourceOrder: [1x1 double] e.g. -1
%
% Structure 'Param' has the following fields:
% Berg: empty
% Center: [3x1 double]
% Conductivity: empty
% EEGType: empty
% Order: [1x1 double] e.g. -1
% Radii: [1x3 double]
%
%
%
% ========================= STUDY: EEG OR MEG DATA =============================
%
% These files should match the template '*data*.mat'
%
% Help for this database file (help_data_data) is given as:
%
% -------------------------- Begin help_data_data ------------------------------
% For m channels of data over n samples of time:
% ChannelFlag : 1 x length(Channel) of {0,1} to indicate whether or not to use
% Warning: when data is measured w.r.t. some reference channel(s),
% ChannelFlag and F (see below) are of length of Channel.
% Channel being the Channel structure stored in a companion
% channel*.mat file in the same fodler as the *data*.mat file.
% Comment : String for human reference 'Simulated Data'
% Device : String information words e.g. 'Neuromag', 'CTF',
% deprecated by still in use by information displays.
% System : String, key words {'CTF','NEUROMAG'};
% Establishes the coordinate system used
% F : The Spatio-temporal length(Channel) x n data matrix in
% MKS units (Telsa, Volt)
% NoiseCov : Sqrt of the noise covariance matrix, m x m (all channels),
% in development
% Projector : empty, in development
% SourceCov : empty, in development
% Time : 1 x n of time indices in seconds
% --------------------------- End help_data_data -------------------------------
%
% Mat-files were found matching this type of file.
% The fieldnames found in these files were:
%
% ChannelFlag
% Comment
% Device
% F
% NoiseCov
% Project
% Projector
% SourceCov
% System
% Time
%
% The files matching this database type were:
%
% default_data\sphere_data_363398.mat
% **(missing fields: Project System)
% jlh_test\JLH_data.mat
% **(missing fields: Project)
% montreal_data\montreal_data_4713.mat
% **(missing fields: Project)
% Sample_Raw\Mixed_data.mat
% **(missing fields: Project)
% simulated\sphere_data_054333.mat
% **(missing fields: Project System)
% test_sphere_files\testsphere_data.mat
% **(missing fields: System)
% USC_Skull\EEG_data6.mat
% **(missing fields: Project)
%
% Loading the first mat-file as a structure yields
%
% 'sphere_data_363398' has the following fields:
% ChannelFlag: [1x138 double]
% Comment: char e.g. 'Simulated Data'
% Device: char e.g. 'Ctf_Axial'
% F: [138x100 double]
% NoiseCov: empty
% Projector: empty
% SourceCov: empty
% Time: [1x100 double]
%
%
%
% ===================== STUDY: INVERSE PROBLEM RESULTS =========================
%
% These files should match the template '*results*.mat'
%
% Help for this database file (help_data_results) is given as:
%
% ------------------------- Begin help_data_results ----------------------------
% Center: [3x1 double]
% Comment: char e.g. 'Simulated data'
% DataFlag : a string specifiying the type of data the results originate from
% 'MEG', 'EEG', 'Fusion'
% Fsynth: [138x100 double]
% IndepTopo: [138x3 double]
% SourceLoc: [1x3 cell]
% SourceOrientation: [1x3 cell]
% Time: [1x100 double]
% TimeSeries: [100x3 double]
% -------------------------- End help_data_results -----------------------------
%
% Mat-files were found matching this type of file.
% The fieldnames found in these files were:
%
% Center
% Channel
% ChannelFlag
% Comment
% DataFile
% DataFlag
% Date
% Fsynth
% Function
% GUI
% HeadModelFile
% ImageGridAmp
% ImageGridTime
% ImagingKernel
% IndepTopo
% ModelGain
% NoiseCov
% OPTIONS
% PatchAmp
% PatchNdx
% Projector
% Residuals
% SourceCorrelation
% SourceCov
% SourceLoc
% SourceOrder
% SourceOrientation
% Study
% StudySubject
% Subject
% Time
% TimeSeries
%
% The files matching this database type were:
%
% default_data\sphere_results_363398.mat
% **(missing fields: Channel ChannelFlag DataFile DataFlag Date Function GUI HeadModelFile ImageGridAmp ImageGridTime ImagingKernel ModelGain NoiseCov OPTIONS PatchAmp PatchNdx Projector Residuals SourceCorrelation SourceCov SourceOrder Study StudySubject Subject)
% default_data\sphere_results_363398_1530.mat
% **(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
% jlh_test\JLH_results_1011.mat
% **(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
% jlh_test\JLH_results_1154.mat
% **(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
% jlh_test\JLH_results_1534.mat
% **(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
% jlh_test\JLH_results_1536.mat
% **(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
% jlh_test\JLH_results_1629.mat
% **(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
% montreal_data\montreal_results_4713_1548.mat
% **(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
% montreal_data\montreal_results_4713_MNE_MEG_1550.mat
% **(missing fields: Center DataFlag GUI IndepTopo SourceCorrelation Study StudySubject Subject)
% simulated\sphere_results_054333.mat
% **(missing fields: Channel ChannelFlag DataFile DataFlag Date Function GUI HeadModelFile ImageGridAmp ImageGridTime ImagingKernel ModelGain NoiseCov OPTIONS PatchAmp PatchNdx Projector Residuals SourceCorrelation SourceCov SourceOrder Study StudySubject Subject)
% test_sphere_files\testsphere_results_1349.mat
% **(missing fields: Center Channel DataFile HeadModelFile ImagingKernel OPTIONS Residuals)
%
% Loading the first mat-file as a structure yields
%
% 'sphere_results_363398' has the following fields:
% Center: [3x1 double]
% Comment: char e.g. 'Simulated data'
% Fsynth: [138x100 double]
% IndepTopo: [138x3 double]
% SourceLoc: [1x3 cell]
% SourceOrientation: [1x3 cell]
% Time: [1x100 double]
% TimeSeries: [100x3 double]
%
%
%
% See also HELP_DATA_BSTSUBJECT, HELP_DATA_IMAGE, HELP_DATA_TESS
% HELP_DATA_TRICONN, HELP_DATA_VERTCONN, HELP_DATA_BSTSTUDY
% HELP_DATA_CHANNEL, HELP_DATA_HEADMODEL, HELP_DATA_DATA
% HELP_DATA_RESULTS
%
%<autobegin> ---------------------- 17-Jun-2004 15:59:48 -----------------------
% --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
%
% CATEGORY: Help
%
% At Check-in: $Author: Mosher $ $Revision: 11 $ $Date: 6/17/04 3:30p $
%
% This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 16-Jun-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> ------------------------ 17-Jun-2004 15:59:48 -----------------------
% CATEGORY: Help
helptext = help(mfilename);
helpwin(mfilename);
Produced by color_mat2html, a customized BrainStorm 2.0 (Alpha) version of mat2html on Tue Oct 12 12:05:14 2004
Cross-Directory links are: ON