Specific research subjects - Revision history

Lof at 07:44, 23 May 2024

2024-05-23T07:44:18Z

← Older revision		Revision as of 07:44, 23 May 2024
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	~~==Saccades==~~		%This page can be deleted
	~~See [https://gitlab.science.ru.nl/marcw/biofysica/-/wikis/home Saccade Cookbook of Marc van Wanrooij].~~

	%~~todo~~

Lof at 09:10, 23 January 2024

2024-01-23T09:10:56Z

← Older revision		Revision as of 09:10, 23 January 2024
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	==Saccades==		==Saccades==
	See [https://gitlab.science.ru.nl/marcw/biofysica/-/wikis/home Saccade Cookbook of Marc van Wanrooij].		See [https://gitlab.science.ru.nl/marcw/biofysica/-/wikis/home Saccade Cookbook of Marc van Wanrooij].

			%todo

Lof: /* Saccades */

2024-01-22T13:05:18Z

Saccades

← Older revision		Revision as of 13:05, 22 January 2024
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	==Saccades==		==Saccades==
			See [https://gitlab.science.ru.nl/marcw/biofysica/-/wikis/home Saccade Cookbook of Marc van Wanrooij].
	[[Saccade Cookbook]]

	~~[[Saccade analysis]]~~

Lof at 13:03, 22 January 2024

2024-01-22T13:03:09Z

← Older revision		Revision as of 13:03, 22 January 2024
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	[[Saccade Cookbook]]		[[Saccade Cookbook]]

	[[Saccade analysis]]		[[Saccade analysis]]

Lof: /* Saccades */

2024-01-22T13:03:02Z

Saccades

← Older revision		Revision as of 13:03, 22 January 2024
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	[[Saccade Cookbook]]		[[Saccade Cookbook]]
			[[Saccade analysis]]

Lof: Replaced content with "==Saccades== Saccade Cookbook"

2024-01-22T12:40:11Z

Replaced content with "==Saccades== Saccade Cookbook"

← Older revision		Revision as of 12:40, 22 January 2024
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	~~<p class~~=~~"clearnone"> A tutorial, for students and coworkers: a recipe to calibrate, detect, and analyze saccades</p>~~		==Saccades==
	~~<hr id~~=~~"system-readmore" />~~

			[[Saccade Cookbook]]
	~~<p class="clearnone">Easily calibrate, detect, and analyze <a href="http://en.wikipedia.org/wiki/~~Saccade" target="_blank">saccades</a> with <a href="<p class="clearnone"> <a href="https://gitlab.science.ru.nl/marcw/biofysica" target="_blank">PANDA</a> tutorial, for students and coworkers: a recipe to calibrate, detect, and analyze saccades</p>">PandA</a>. For a more detailed description, visit the other <a href="http://www.neural-code.com/index.php/panda/action/saccade">saccade</a> sections, starting with the <a href="http://www.neural-code.com/index.php/panda/action/87-saccade/70">introduction</a>.</p>

	~~<h2>Calibration</h2>~~
	~~<p>First you have to calibrate (see also saccade <a href="http://www.neural-code.com/index.php/tutorials/action/saccade/55-saccade-calibration">calibration</a>)~~
	~~by training an artificial neural netwok to learn the relationship between measured voltages and head orientation:~~
	~~<pre xml:lang="matlab">pa_calibrate</pre>~~
	~~<p>(choose the calibration dat-file in the pop-up menu, usually ending in 0000).~~
	~~Then you can calibrate (and low-pass filter) the data-files, by using the button in the pa_calibrate interface~~
	~~(this will calibrate ALL dat-files with the .net-file you got from the pa_calibrate-procedure). </p>~~

	~~<h2>Detection</h2>~~
	~~<p>Then you have to detect (see also saccade <a href="http://www.neural-code.com/index.php/tutorials/action/saccade/56-saccade-detection">detection</a>)~~
	~~with:~~
	~~<pre xml:lang="matlab"> pa_sacdet</pre>~~
	~~<p>(choose an experimental hv-file, usually ending with numbers 0001 and up). </p>~~
	~~<h2>Parameters</h2>~~
	~~<p>Obtain all movement parameters, such as end-point location, reaction time, peak velocity. </p>~~
	~~<pre xml:lang="matlab"> pa_sac2mat</pre>~~
	~~(these will be saved in a mat-file)</p>~~

	~~<h2>Analysis</h2>~~
	~~<p>Finally, you can start some high-level analysis (see also saccade <a href="http://www.neural-code.com/index.php/tutorials/action/saccade/54-saccade-analysis">analysis</a>)~~
	~~After all these obligatory steps, you can actually start analyzing the data. This usually involves custom-made analysis functions, suited for your experiment. First you have to load the data:~~
	~~<pre xml:lang="matlab"> load MW-RG-2011-03-02-0001</pre>~~
	<p>You will now have a Sac- and a Stim-matrix. The Sac-matrix contains all the movement parameters, the Stim-matrix all the stimulus parameters. You can combine them into a single matrix, containing in each column a relevant parameter, and each row containing a single saccade.</p>
	~~<pre xml:lang="matlab"> SupSac = pa_supersac(Sac,Stim,XX,YY);</pre>~~
	~~<p>Note that the XX and YY should be numbers describing the type of stimulus, and the number of that type of stimulus in the trial, e.g.~~
	~~<pre xml:lang="matlab"> SupSac = pa_supersac(Sac,Stim,1,2);</pre>~~
	~~<p>for the second (YY=2) stimulus of type 1 (XX=1, usually an LED) in a trial, or</p>~~
	~~<pre xml:lang="matlab"> SupSac = pa_supersac(Sac,Stim,2,1);</pre>~~
	~~<p>for the first (YY=1) stimulus of type 2 (XX=2, usually a sound) in the trial (you have to check what number is assigned to which stimulus type, by typing:~~
	~~<pre xml:lang="matlab"> help pa_readcsv</pre>~~
	~~in the trial information of the LOG-matrix, line 5).</p>~~
	~~<p>To plot target location versus response location :</p>~~
	~~<pre xml:lang="matlab"> plot(SupSac(:,23),SupSac(:,8),’k.’);</pre>~~
	~~<p>or</p>~~
	~~<pre xml:lang="matlab">pa_plotloc(SupSac);</pre>~~

Lof: Created page with "
A tutorial, for students and coworkers: a recipe to calibrate, detect, and analyze saccades

Easily..."

2024-01-22T12:37:03Z

Created page with "<p class="clearnone"> A tutorial, for students and coworkers: a recipe to calibrate, detect, and analyze saccades</p> <hr id="system-readmore" /> <p class="clearnone">Easily..."

New page

<p class="clearnone"> A tutorial, for students and coworkers: a recipe to calibrate, detect, and analyze saccades</p>
<hr id="system-readmore" />

<p class="clearnone">Easily calibrate, detect, and analyze <a href="http://en.wikipedia.org/wiki/Saccade" target="_blank">saccades</a> with <a href="<p class="clearnone"> <a href="https://gitlab.science.ru.nl/marcw/biofysica" target="_blank">PANDA</a> tutorial, for students and coworkers: a recipe to calibrate, detect, and analyze saccades</p>">PandA</a>. For a more detailed description, visit the other <a href="http://www.neural-code.com/index.php/panda/action/saccade">saccade</a> sections, starting with the <a href="http://www.neural-code.com/index.php/panda/action/87-saccade/70">introduction</a>.</p>

<h2>Calibration</h2>
<p>First you have to calibrate (see also saccade <a href="http://www.neural-code.com/index.php/tutorials/action/saccade/55-saccade-calibration">calibration</a>)
by training an artificial neural netwok to learn the relationship between measured voltages and head orientation:
<pre xml:lang="matlab">pa_calibrate</pre>
<p>(choose the calibration dat-file in the pop-up menu, usually ending in 0000).
Then you can calibrate (and low-pass filter) the data-files, by using the button in the pa_calibrate interface
(this will calibrate ALL dat-files with the .net-file you got from the pa_calibrate-procedure). </p>

<h2>Detection</h2>
<p>Then you have to detect (see also saccade <a href="http://www.neural-code.com/index.php/tutorials/action/saccade/56-saccade-detection">detection</a>)
with:
<pre xml:lang="matlab"> pa_sacdet</pre>
<p>(choose an experimental hv-file, usually ending with numbers 0001 and up). </p>
<h2>Parameters</h2>
<p>Obtain all movement parameters, such as end-point location, reaction time, peak velocity. </p>
<pre xml:lang="matlab"> pa_sac2mat</pre>
(these will be saved in a mat-file)</p>

<h2>Analysis</h2>
<p>Finally, you can start some high-level analysis (see also saccade <a href="http://www.neural-code.com/index.php/tutorials/action/saccade/54-saccade-analysis">analysis</a>)
After all these obligatory steps, you can actually start analyzing the data. This usually involves custom-made analysis functions, suited for your experiment. First you have to load the data:
<pre xml:lang="matlab"> load MW-RG-2011-03-02-0001</pre>
<p>You will now have a Sac- and a Stim-matrix. The Sac-matrix contains all the movement parameters, the Stim-matrix all the stimulus parameters. You can combine them into a single matrix, containing in each column a relevant parameter, and each row containing a single saccade.</p>
<pre xml:lang="matlab"> SupSac = pa_supersac(Sac,Stim,XX,YY);</pre>
<p>Note that the XX and YY should be numbers describing the type of stimulus, and the number of that type of stimulus in the trial, e.g.
<pre xml:lang="matlab"> SupSac = pa_supersac(Sac,Stim,1,2);</pre>
<p>for the second (YY=2) stimulus of type 1 (XX=1, usually an LED) in a trial, or</p>
<pre xml:lang="matlab"> SupSac = pa_supersac(Sac,Stim,2,1);</pre>
<p>for the first (YY=1) stimulus of type 2 (XX=2, usually a sound) in the trial (you have to check what number is assigned to which stimulus type, by typing:
<pre xml:lang="matlab"> help pa_readcsv</pre>
in the trial information of the LOG-matrix, line 5).</p>
<p>To plot target location versus response location :</p>
<pre xml:lang="matlab"> plot(SupSac(:,23),SupSac(:,8),’k.’);</pre>
<p>or</p>
<pre xml:lang="matlab">pa_plotloc(SupSac);</pre>

Specific research subjects - Revision history

Lof at 07:44, 23 May 2024

Lof at 09:10, 23 January 2024

Lof: /* Saccades */

Lof at 13:03, 22 January 2024

Lof: /* Saccades */

Lof: Replaced content with "==Saccades== Saccade Cookbook"

Lof: Created page with " A tutorial, for students and coworkers: a recipe to calibrate, detect, and analyze saccades Easily..."

Lof: Created page with "
A tutorial, for students and coworkers: a recipe to calibrate, detect, and analyze saccades

Easily..."