Paradigm File Format in BESA - Revision history

Robert at 06:38, 6 May 2021

2021-05-06T06:38:39Z

Jaehyun: /* Thresholds */

2020-08-26T10:00:21Z

‎Thresholds

Jaehyun: /* Artifact Scan */

2020-08-26T09:58:42Z

‎Artifact Scan

Jaehyun: /* Detailed description of the sections */

2020-08-26T09:48:54Z

‎Detailed description of the sections

Jaehyun: /* General remarks */

2018-05-04T11:20:29Z

‎General remarks

Jaehyun: /* Artifact Scan */

2018-05-04T11:19:41Z

‎Artifact Scan

Jaehyun: /* Artifact Scan */

2018-05-04T11:17:05Z

‎Artifact Scan

Jaehyun: /* General remarks */

2018-04-09T13:43:15Z

‎General remarks

Robert at 14:06, 15 February 2017

2017-02-15T14:06:59Z

Todor at 13:51, 12 May 2016

2016-05-12T13:51:25Z

@@ Line 2: / Line 2: @@
 |title = Module information
 |module = BESA Research Basic or higher
-|version = 5.2 or higher
+|version = BESA Research 5.2 or higher
 }}

@@ Line 142: / Line 142: @@
 This section holds values for artifact rejection. It can hold two sets of values. The first set contains settings for the color normalization of the BESA artifact scan tool. These values are not directly used for artifact rejection, but merely for visual control if the BESA artifact scan tool is used for artifact rejection.
-The line following the first set of values contains either the string “AUTO_REJECT”, or “MANUAL_REJECT”.
+The line following the first set of values contains either the string <code>AUTO_REJECT</code>, or <code>MANUAL_REJECT</code>.
-The second set contains settings for automatic rejection of artifacts. It is used if the preceding line contains the string “AUTO_REJECT”. Otherwise, only artifacts which were manually marked in the data are excluded from the averaging process.
+The second set contains settings for automatic rejection of artifacts. It is used if the preceding line contains the string <code>AUTO_REJECT</code>. Otherwise, only artifacts which were manually marked in the data are excluded from the averaging process.
 The following table gives the order of the entries in the thresholds section:
@@ Line 200: / Line 200: @@
 The unit &part;T stands for the sampling interval.
-'''Example:'''
+Example:
 <source lang="dos">
 [Thresholds]

@@ Line 678: / Line 678: @@
 {{font color|green|7.55 6.71 7.55 7.55 4.20 9.23 11.75 7.55 8.39 8.39 7.55 0.00}}
 This example contains the first 2 epochs from an artifact scan.
 {{font color|blue|65	0	0}}
 This line shows the number of EEG (65), MAG and GRA channels.
 {{font color|red|0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0}}
@@ Line 694: / Line 697: @@
 This line shows the badness of the channels. One channel has badness 8, which stands for gradient and integral criterion.
 {{font color|deeppink|2	1	2}}
 This line states the number of conditions in the artifact scan list, and their indices: There are 2 conditions; the list element 0 contains condition 1, list element 1 contains condition 2. Condition 0 is not part of the scan.
 {{font color|green|0.000000	319120000.000000}}
@@ Line 703: / Line 708: @@
 A range from 0 – 319.120 seconds was scanned.
 The next lines give the values for the epochs in groups of 4:
 {{font color|blue|0	7700000.00}}
 This entry has artifact list index 0 (which corresponds to condition index 1, see above), and the position of the epoch is 7.700000 seconds.
 The next 3 lines hold amplitudes, variances, and gradients for each channel.
-</blockquote>
 [[Category:ERP/ERF]] [[Category:Data Import/Export]]

@@ Line 52: / Line 52: @@
 == Detailed description of the sections ==
 === Attributes ===
 This section is mandatory.
 It holds the attributes which are used to group the trigger events. The first attribute is always the trigger code (“code”). Attributes are separated by a tabulator. By default, the ERP module defines a second attribute “name” which can take trigger names as attribute values.
-'''Example:'''
+Example:
 <source lang="dos">
 [Attributes]
 code	name	modality
 </source>
 === Values ===
 This section holds a table of attribute values which are defined for the triggers used in the experiment. Each row defines one trigger. The first column holds the trigger codes, since the trigger code is the only mandatory attribute. The second column holds the values for the second attribute (default in the ERP module: name), and so on. If no value is defined for an attribute, “NULL” is entered. For trigger codes which are not listed, no values are defined.
-'''Example:'''
+Example:
 <source lang="dos">
 [Values]
@@ Line 78: / Line 80: @@
 This section holds the names of conditions which are defined in detail in the section “Selections”. It is not necessary to give names to conditions. By default, conditions are simply named “Condition 1” through “Condition 32”. If a name is given, it is followed by the zero-based index of the condition it refers to. This enables mixing of conditions with user-given names and conditions with default names.
-'''Example:'''
+Example:
 <source lang="dos">
 [Names]
@@ Line 90: / Line 92: @@
 This section holds the averaging epochs for each condition. Furthermore, additional epochs can be specified. Each epoch is defined by a floating point value which gives the pre-stimulus interval in milliseconds (ms), and a second floating point value which gives the post-stimulus interval in ms. Epochs are given in the following order:
-'''Averaging epoch:''' 	The epoch used for averaging
+* '''Averaging epoch''': The epoch used for averaging
+* '''Baseline epoch''': The epoch over which the baseline is calculated
-'''Baseline epoch:'''	The epoch over which the baseline is calculated
+* '''Epoch used for artifact rejection''': The epoch in which the data are checked for artifacts
+* '''Stimulus artifact epoch''': An epoch where a stimulus artifact occurred. This epoch is interpolated over before artifact rejection takes place
-'''Epoch used for artifact rejection:'''	The epoch in which the data are checked for artifacts
+* '''Stimulus delay''': Only one value. This value gives the delay of the stimulus relative to the trigger event (e.g. when tactile stimulation is performed, where air pressure builds up after the trigger was set).
-−
-'''Stimulus artifact epoch:'''	An epoch where a stimulus artifact occurred. This epoch is interpolated over before artifact rejection takes place
-−
-'''Stimulus delay:'''	Only one value. This value gives the delay of the stimulus relative to the trigger event (e.g. when tactile stimulation is performed, where air pressure builds up after the trigger was set).
 Not all epochs have to be provided. If the epochs list for a condition is incomplete, default values are used.
@@ Line 130: / Line 128: @@
 |}
-'''Example:'''
+Example:
 <source lang="dos">
 [Epochs]
@@ Line 137: / Line 135: @@
 </source>
-The first condition is averaged from 500ms before the trigger event to 1000ms after the trigger event. Baseline is calculated in the pre-stimulus interval between 100ms before the trigger event and the trigger event. Artifacts are rejected between –500ms and +1000ms, i.e. over the entire averaging epoch. No stimulus artifact interval and no stimulus delay is given.
+The first condition is averaged from 500 ms before the trigger event to 1000 ms after the trigger event. Baseline is calculated in the pre-stimulus interval between 100 ms before the trigger event and the trigger event. Artifacts are rejected between –500 ms and +1000 ms, i.e. over the entire averaging epoch. No stimulus artifact interval and no stimulus delay is given.
-For the second condition, averaging and artifact rejection are set to –800...500 ms, and baseline calculation is performed in the interval from –800ms to –700ms. Again, no stimulus artifact interval, and no stimulus delay is given.
+For the second condition, averaging and artifact rejection are set to –800...500 ms, and baseline calculation is performed in the interval from –800 ms to –700 ms. Again, no stimulus artifact interval, and no stimulus delay is given.
 === Thresholds ===
@@ Line 267: / Line 265: @@
 If more than one bit is set, a different averaging buffer will be created for each sub-set.
-'''Example:'''
+Example:
 <source lang="dos">
 [Averaging]
@@ Line 275: / Line 273: @@
 One condition was selected. The second condition (condition index 1) is selected and activated, and two buffers will be averaged: the first buffer for all matching sweeps (bit 0 set), the second buffer for the first half of matching sweeps (bit 3 set).
 === Filter ===
 This section holds filter settings which were chosen for averaging. The following table gives the possible settings.
@@ Line 382: / Line 381: @@
 If any of the required settings are missing, the filters that are currently set in the data file are used for averaging.
-'''Example:'''
+Example:
 <source lang="dos">
 [Filter]
@@ Line 415: / Line 414: @@
 === TimeFrequency ===
 This section holds the settings of the Time-Frequency dialog. It is only read if the time-frequency module is loaded. The following values are stored:
@@ Line 494: / Line 492: @@
 |}
-'''Example:'''
+Example:
 <source lang="dos">
 [TimeFrequency]
@@ Line 533: / Line 531: @@
 Operators can be AND, OR. Bracketing is also possible.
-'''Example:'''
+Example:
 <source lang="dos">
 [Selections]
@@ Line 562: / Line 560: @@
 === Artifact Scan ===
 This section holds the results of an artifact scan. They are plotted in the artifact tab central window. For each epoch which was scanned, all values are written. The format contains 4 header lines, followed by 4 lines for each epoch:
@@ Line 602: / Line 599: @@
 Line 4: <Start of scanned range (position in microseconds)><end of scanned range (position in microseconds>
 </blockquote>
@@ Line 621: / Line 617: @@
-'''Example:'''
+Example:
 Please note that one color denotes one line in the PDG-file.

@@ Line 13: / Line 13: @@
 The PDG file is written in ASCII format and can thus be viewed and edited in any text editor. It is subdivided into a maximum of 9 sections:
 {|
 |-
@@ Line 35: / Line 36: @@
 | [ArtifactScan] || The artifact scan results are written here.
 |}
 Most sections can be omitted; their entries are then filled with default values. The default settings are given in the detailed description (see below). The most relevant sections for describing an experiment are '''Attributes''', '''Values''', and '''Selections'''.

@@ Line 563: / Line 563: @@
 This section holds the results of an artifact scan. They are plotted in the artifact tab central window. For each epoch which was scanned, all values are written. The format contains 4 header lines, followed by 4 lines for each epoch:
-<blockquote style="background-color: lightgrey; border: solid thin grey;">
+<blockquote style="background-color: #f9f9f9; border: solid thin lightgrey;">
 Line 1: <Number of EEG channels> <Number of magnetometer or axial gradiometer channels> <Number of planar gradiometer channels>
@@ Line 605: / Line 605: @@
 The remaining lines come in groups of 4. Each group contains the settings for one epoch. For each epoch:
-<blockquote style="background-color: lightgrey; border: solid thin grey;">
+<blockquote style="background-color: #f9f9f9; border: solid thin lightgrey;">
 Line 1: <artifact scan list index><position in microseconds>
@@ Line 623: / Line 623: @@
 Please note that one color denotes one line in the PDG-file.
-<blockquote style="background-color: Gainsboro; border: solid thin grey;">
+<blockquote style="background-color: #f9f9f9; border: solid thin lightgrey;">
 [ArtifactScan]

@@ Line 12: / Line 12: @@
 The PDG file is written in ASCII format and can thus be viewed and edited in any text editor. It is subdivided into a maximum of 9 sections:
-# [Attributes] 	Attributes which are used to group the trigger events. This section is mandatory.
-# [Values]	A table of attribute values which are defined for the triggers used in the experiment.
+{|
-# [Names]	Names of conditions which are defined in detail in section 8
+|-
-# [Epochs]	For each condition, averaging epochs, baseline epochs, and some other epochs are defined
+| width="140pt" | [Attributes] || Attributes which are used to group the trigger events. This section is mandatory.
-# [Thresholds]	Threshold settings used for artifact rejection
+|-
-# [Averaging]	Defines which conditions are selected for averaging
+| [Values] || A table of attribute values which are defined for the triggers used in the experiment.
-# [Filter]		Filter settings for averaging
+|-
-# [TimeFrequency]	Settings for time-frequency analysis
+| [Names] || Names of conditions which are defined in detail in section 8
-# [Selections]	Each condition is written here as a statement using Boolean logic
+|-
-# [ArtifactScan] The artifact scan results are written here
+| [Epochs] || For each condition, averaging epochs, baseline epochs, and some other epochs are defined.
 Most sections can be omitted; their entries are then filled with default values. The default settings are given in the detailed description (see below). The most relevant sections for describing an experiment are '''Attributes''', '''Values''', and '''Selections'''.

← Older revision		Revision as of 14:06, 15 February 2017
Line 690:		Line 690:
	The next 3 lines hold amplitudes, variances, and gradients for each channel.		The next 3 lines hold amplitudes, variances, and gradients for each channel.

−	[[Category:ERP/ERF]]	+	[[Category:ERP/ERF]] [[Category:Data Import/Export]]

← Older revision		Revision as of 13:51, 12 May 2016
Line 1:		Line 1:
		+	{{BESAInfobox
		+	\|title = Module information
		+	\|module = BESA Research Basic or higher
		+	\|version = 5.2 or higher
		+	}}

	== General remarks ==		== General remarks ==
Line 684:		Line 689:

	The next 3 lines hold amplitudes, variances, and gradients for each channel.		The next 3 lines hold amplitudes, variances, and gradients for each channel.
		+
		+	[[Category:ERP/ERF]]