TSG Doc - User contributions [en]

Informed consent

2025-11-14T15:22:33Z

Wilbert.vanham: /* Limesurvey example */

== Informed consent ==
We have an updated [https://www.radboudnet.nl/socialsciences/research/ethics-committee-social-science/informed-consent/ informed consent procedure] for research reviewed by the [https://www.radboudnet.nl/socialsciences/research/ethics-committee-social-science/ Ethical Committee of Social Sciences (ECSS)] as of November 2025.

The following changes have been implemented:
* Generic templates for RU/Faculty of Social Sciences, with shorter and better understandable texts, available via ECSS website
* Based on these templates researchers compile their own study-specific general information brochure and consent forms
* Updates to the screening form and Adverse Events Procedure

The source documents:
* [[File:Informed consent slides.pdf|thumb|Slides]] of the information session.
* [[File:Informed consent instructions.docx|thumb|Instructions]] for completing the table.
* [[File:Informed consent template.docx|thumb|Template]] information document and consent form, Ethics Committee Social Sciences, Version 1.0 November 2025

Feel free to reach out to [https://www.ru.nl/personen/kos-m Miriam Kos] in case of any questions.

== Implementation ==
Since this procedure no longer uses standard forms supplied by the Institute, you will have to include the information brochure and consent form in your own experiment.
For two common online experiment systems (Limesurvey and jsPsych) we give an example how to include such a form here.

Feel free to contact [https://www.ru.nl/personen/ham-w-van me] for questions.
=== Limesurvey example ===
[https://questions.socsci.ru.nl/index.php/245182 Demo survey] for the informed consent form with all elements. For anonymous studies all questions can be removed. For non-anonymous studies the first questions must be present. Note that only the first question is validated at the moment. You can validate the second question as well for medical studies. There is no Dutch version yet.

=== jsPsych example ===

Informed consent

2025-11-14T14:24:55Z

Wilbert.vanham: /* Limesurvey example */

2025-10-06T13:38:41Z

ButtonBox

2023-08-29T11:21:09Z

Wilbert.vanham: /* Python/PsychoPy */

{{Infobox tsg
| name = Buttonbox (2018)
| image = Buttonbox_2018_1.png
| caption = 2018 Buttonbox
| downloads = {{bulleted list
| [https://surfdrive.surf.nl/files/index.php/s/PPTKCyrjLkN4XUO Buttonbox 2018]
| [https://pypi.python.org/pypi/RuSocSci RuSocSci] (Python package)
}}
}}
{{Infobox tsg
| name = Buttonbox
| image = Buttonbox 03s.png
| caption = 2013 Buttonbox
| downloads = {{bulleted list
| [https://surfdrive.surf.nl/files/index.php/s/72XEcu2XKSgzxjp Buttonbox 2015]
| [https://pypi.python.org/pypi/RuSocSci RuSocSci] (Python package)
}}
}}

The buttonbox is used for time accurate(1ms) button press registration. We use it to register buttonpresses, soundkey, voicekey signals and to send tone onset, analog output, triggers with the BITSI protocol. It is suitable for Behavioral, EEG, MEG, and fMRI experiments. The buttonbox is connected to a computer with a usb connection.

The output connector has two binary eight bit ports: input and output. The two ports can be used for responses (input) and stimulus triggers (output). Two 12 bits analog outputs and three 12 bits analog inputs. The output connector has a sound and voicekey which triggers when a amplitude reaches a threshold. By using the serial port, the BITSI can be used platform independently: it works on Windows, Linux and Mac OSX. Most programming environments and stimulus packages support serial communication.

There is currently a [[Microsoft Windows driver issue]].

== BITSI Protocol ==

BITSI stands for Bits to Serial Interface. Because the BITSI is designed to interface both in- and output signals, the 'protocol' is asymmetric: the input and output protocols differ.

===Input===

The input port can be used to interface eight buttons maximally. Button presses are translated to serial output characters/bytes according to the following table:

{| class="wikitable"
|-
! scope="row" colspan="3" | BITSI Simple
|-
! scope="row" width="120px" | Signal/Button
! scope="row" width="120px" | ASCII (rise/fall)
! scope="row" width="120px" | Code (rise/fall)
|-
| 1 || A / a || 65 / 97
|-
| 2 || B / b || 66 / 98
|-
| 3 || C / c || 67 / 99
|-
| 4 || D / d || 68 / 100
|-
| 5 || E / e || 69 / 101
|-
| 6 || F / f || 70 / 102
|-
| 7 || G / g || 71 / 103
|-
| 8 || H / h || 72 / 104
|-
|}

This means that when signal 1 gets active(button press), a capital A will be sent to the serial port. A lowercase 'a' will be sent when the signal is deactivated(button release). Mechanical buttons can be connected directly.

===Output===

Output knows two protocols: '''BITSI simple''' or '''BITSI extended'''. To enter a certain protocol two buttons have to be pressed when the BITSIbox is powered or com port opens. '''[2015]Press button H and A for simple mode and H and B for extended mode. [2018]Press button E and A for simple mode and E and B for extended mode.'''

If no button is pressed when powered it boots the last known protocol. In the simple protocol every byte sent to the BITSI over the serial port, is represented at the 8 bit output.

The '''extended''' protocol uses two bytes(or two characters), this combination can access two analog outputs and a tone generator. The first byte selects the output. The second byte determines the value written to this output.

{| class="wikitable"
|-
! scope="row" colspan="3" | BITSI Extended
|-
! scope="row" width="120px" | Function
! scope="row" width="150px" | Byte 1 (ASCII/code)
! scope="row" width="150px" | Byte 2
|-
| Marker Out || M / 77 || Marker Value
|-
| Pulse Out || P / 80 || Marker Value
|-
| Pulse Time || X / 88 || ms before pulse reset
|-
| Analog Out 1 || Y / 89 || Analog Output Value
|-
| Analog Out 2 || Z / 90 || Analog Output Value
|-
| Tone || T / 84 || Start Tone
|-
| Detect Sound || D / || S / 83
|-
| Detect Voice || D / || V / 83
|-
| Calibrate Sound || C / || S
|-
| Calibrate Voice || C / || V
|-
| Analog In 1 || A / || 1
|-
| Analog In 2 || A / || 2
|-
| Analog In 3 || A / || 3
|-
| Analog In 4 || A / || 4
|-
| LEDs Off || L / || X
|-
| LEDs Input || L / || I
|-
| LEDs Output || L / || O
|-
|}

== Port Settings ==

===Trigger port ===

[[File:Connector.png|thumb|300x300px|Schematic view of the 25 pins connector]]

The 25 pins female connector has 8 inputs and 8 outputs, respectively 1-8 are inputs and 9-16 are outputs. Three analog input with an analog to digital convertor of 12 bit, pins 17,18,20 and 21. Two analog outputs with an digital to analog convertor of 12 bits on pins 22 and 23.

The inputs 1-8 will be pulled down from 5V to GND when the buttons are pressed. The outputs 9-16 will be pulled up from GND to 5V when the output is activated.

===Serial port===

Our hardware design allows to be connected to the computers USB and emulates a serial communication Port.

{| class="wikitable"
|-
| Baudrate || 115200
|-
| Parity || None
|-
| Data bits || 8
|-
| Stop bits || 1
|-
| Flow control || None
|-
|}

=== USB-Com port ===

1.Connect the BITSIbox to your computer using the USB cable.

2.When you connect the BITSIbox, Windows should initiate the driver installation process (if you haven't used the computer with an BITSIbox board before).

3.On Windows Vista/7, the driver should be automatically downloaded and installed.

4.On Windows XP, the Add New Hardware wizard will open:

*When asked '''Can Windows connect to Windows Update to search for software?''' select '''No, not this time'''. Click next.
*Select '''Install from a list or specified location (Advanced)''' and click next.
*Make sure that '''Search for the best driver in these locations''' is checked; uncheck '''Search removable media'''; check '''Include this location in the search''' and browse to the '''c:/beheer/arduino/drivers '''directory.
*The wizard will search for the driver and then tell you that a "USB Serial Converter" was found. Click finish.
*The new hardware wizard will appear again. Go through the same steps and select the same options and location to search. This time, a "USB Serial Port" will be found.

'''How to Check the Com Port settings(important!)'''

*From the Start menu, open the '''Control Panel'''.

*From the control panel, open the '''System window'''.

*From the system properties window, go to the '''Hardware tab''' and click the '''Device Manager''' button.

*From the Device Manager window, click '''Ports (Com&LPT).''' You should now be able to see which Com Port the USB adapter is assigned to.

*If the Com Port is 10 or higher, you will have to change it to a lower port.

*From the Device Manager window, click on '''USB Serial Port (Com#).''' Click the '''Port Settings tab''' of the USB Serial Port Properties window, and then click the '''Advanced''' button.

*In the Advanced Settings window, use the scroll input to select a '''Com Port''' (select 10 or lower). Change '''Receive (bytes)''' and '''Transmit (bytes)''' to 64. Change the '''Latency Timer''' to 1.

*Click the OK button.

Always connect the usb device to the same port and your settings will be remembered.

== Software Settings ==

=== Neurobs Presentation ===

The experiment files needs a few settings for the device to work:
* In the settings tab: port -> input port -> 1 must be the device that identifies itself as "Arduino Uno" in the device manager. Note that the port must have a number not higher than 10 (COM1-COM10). Use re-enumerate if it is higher.
* Rate must be set 115200, Parity to None, Data Bits to 8 and Stop Bits to 1, Uncheck FIFO Interrupt.

[[File:Buttonbox2.png]]

'''Testing Buttonbox'''

When pressing on the A button within the input channel tester. You will see the following ASCII code.

[[file:testbuttonbox.png]]

'''Adding Marker'''

[[file:output_buttonbox1.png | 800px]]

'''Testing Markers (output)'''

Send code 1 for Button A

[[file:output_buttonbox2.png]]

Button A will light up.

[[file:buttonboxledA.png | 200px]]

Send code 0 for clearing.

[[file:output_buttonbox3.png]]

'''Example PCL code you can program a handle to send a marker:'''

#handle:
output_port OutputPort = output_port_manager.get_port( 1 );

'''Example to send a marker:'''
OutputPort.send_code(100); #create a marker

for more information see chapter 8 in the presentation course by clicking [http://tsgdoc.socsci.ru.nl/images/9/9e/Programming_with_Presentation_2013.pdf here]

=== Python/PsychoPy ===

Download this site-package to use the buttonbox: [https://pypi.python.org/pypi/RuSocSci rusocsci]

or use in windows command 'pip install --upgrade rusocsci'

'''Example using buttons from the buttonbox in Python:'''

<syntaxhighlight lang="python" line>
#!/usr/bin/env python

# import the rusocsci.buttonbox module
from rusocsci import buttonbox

# make a buttonbox
bb = buttonbox.Buttonbox()

# wait for a single button press
b = bb.waitButtons()

# print the button pressed
print("b: {}".format(b))
</syntaxhighlight>

'''Example using markers with the buttonbox in Python:'''

<syntaxhighlight lang="python" line>
#!/usr/bin/env python

# import the rusocsci.buttonbox module
from rusocsci import buttonbox

# make a buttonbox
bb = buttonbox.Buttonbox()

# send a marker
bb.sendMarker(val=100) #This is your marker code, range code 1-255
</syntaxhighlight>

'''Example using BITSI extended in Python:'''

<syntaxhighlight lang="python" line>
#!/usr/bin/env python

# import the rusocsci.buttonbox module
from rusocsci import buttonbox

# make a buttonbox
bb = buttonbox.Buttonbox()

# select a function
bb.sendMarker(val=(ord('X'))) #select pulse time
bb.sendMarker(val=2) #set time of dureation pulse to 2ms

bb.sendMarker(val=(ord('M'))) #select marker out
bb.sendMarker(val=115) #set marker value 115
</syntaxhighlight>

'''Example using BITSI extended analog read in Python:'''

<syntaxhighlight lang="python" line>
#!/usr/bin/env python

# import the rusocsci.buttonbox module
import serial

# make a buttonbox
ser = serial.Serial("COM2", 115200, timeout = 0.10 )
ser = serial.Serial("/dev/ttyUSB0", 115200, timeout = 0.10 )

while True:
ser.write('A1')
ser.flush()
x = ser.readline()
visual.TextStim(win, text=x).draw()

# black screen for 1000 ms
win.flip()

key = event.getKeys()
try:
if key[0]=='escape':
break
except:
continue
</syntaxhighlight>

 '''Example using the Buttonbox in PsychoPy:'''

<syntaxhighlight lang="python" line>
#!/usr/bin/env python

# import psychopy and rusocsci
from psychopy import core, visual
from rusocsci import buttonbox

## Setup Section
win = visual.Window(monitor="testMonitor")
bb = buttonbox.Buttonbox()
text = visual.TextStim(win, "Press a button on the buttonbox")

## Experiment Section
# show text
text.draw()
win.flip()
# wait for response
b = bb.waitButtons()
# show response
text.setText("you pressed: {}".format(b))
text.draw()
win.flip()
core.wait(5)

## Cleanup Section
core.quit()
</syntaxhighlight>

For more documentation click here: http://pythonhosted.org//RuSocSci/index.html
 
 

=== Matlab ===
'''Example using markers with the Buttonbox in Matlab:'''

Download the file Bitsi.m from the DCCN website: https://intranet.donders.ru.nl/index.php?id=bitsim0
 Make sure to have this file in your Matlab path.
<syntaxhighlight lang="matlab" line style="overflow:auto;">
% At the start of your script, create the buttonbox serial object
bb = Bitsi("COM2");
% other code
:
</syntaxhighlight>

BITSI simple mode:
<syntaxhighlight lang="matlab" line style="overflow:auto;">
% This example is for an EEG system sampling at 500Hz samplerate.
% at the start of your script, reset marker
samplerate = 500;
pulseLen = 2000/samplerate;
bb.sendTrigger(0);
% send a marker
val = 1; % val: this is your marker code, range code 1-255
bb.sendTrigger(val);
java.lang.Thread.sleep(pulseLen); % wait long enough for the EEG system to capture the trigger, i.e., 2000/samplerate ms
% reset marker
bb.sendTrigger(0) % Note: if resetting the marker is not possible at this moment in code, you can decide to do this later as long as it has taken place long enough before the next marker has to be sent. Another solution using a timer object instead of a simple delay is outlined below.
</syntaxhighlight>

BITSI extended mode:
<syntaxhighlight lang="matlab" line style="overflow:auto;">
samplerate = 500;
pulseLen = 2000/samplerate;
% select a function
bb.sendTrigger(uint8('X')); % select pulse time
bb.sendTrigger(pulseLen); % set time of duration pulse to (2000/samplerate) ms

val = 1; % val: this is your marker code, range code 1-255
bb.sendTrigger(uint8('M')); % select marker out
bb.sendTrigger(val); % val: this is your marker code, range code 1-255
</syntaxhighlight>

<syntaxhighlight lang="matlab" line style="overflow:auto;">
% At the end of your script, close the buttonbox serial object
:
bb.close();
</syntaxhighlight>

Reset marker using a timer:
<syntaxhighlight lang="matlab" line style="overflow:auto;">
% At the start of your script, define timer object and callback function
pulseTime = 0.004; % trigger pulse duration in s. NB: extra time will be added due to overhead in calling Matlab functions related to the timer event.
resetMarker = timer('TimerFcn',@(x,y)bb.sendTrigger(0),'StartDelay',pulseTime);

% replace the code to send a marker with:
val = 1; % val: this is your marker code, range code 1-255
bb.sendTrigger(val);
resetMarker.start(); % this will call bb.sendTrigger(0) after pulseTime seconds (plus some additional overhead)

</syntaxhighlight>

2023-06-13T21:53:48Z

Wilbert.vanham: /* Sequence */

=== Sequence ===
[https://www.socsci.ru.nl/tsg/sequence Sequence] Allows you to send the same data as URL parameters to a num,bers of URLs that together make up your experiment. Typically You will start from SONA or Prolific, then go to an informed consent form, then to an online experiment or survey and then back to Prolific for completion of the experiment.
[[File:Prolific URL.png|frame|left|form on the prolific study page showing the experiment url.]]

[[File:Prolific completion.png|frame|left|Form on the Prolific study page showing the completion URL.]]

2022-03-23T10:29:11Z

Wilbert.vanham: updating to limesurvey 5

{{Infobox software
| name = LimeSurvey
| logo = Limesurvey_logo.png
| logo size = 200px
| logo alt = Limesurvey
| screenshot = Limesurvey_screenshot01.jpg
| caption = A Limesurvey survey with the Radboud template
| developer =
| installed version = 5
| installed version date = 
| platform = Web
| language count = 84
| website = [http://limesurvey.org limesurvey.org]
| resources =
{{Infobox tsg
| child = yes
| header2 = Radboud Survey 5
| data2 = *[https://questions.socsci.ru.nl/admin Admin Login]
| manuals = {{bulleted list
| [http://manual.limesurvey.org/ Manual]
}}
}}
}}
== General ==
LimeSurvey is a popular open source system for making and publishing surveys. All students and staff of the Faculty of Social Sciences can use it.

Log on to [https://questions.socsci.ru.nl/index.php/admin questions.socsci.ru.nl/admin] with your university number and password to make a survey. Invitations to surveys can be send with a direct link to the survey (e.g. ''[https://questions.socsci.ru.nl/index.php/123456 https://questions.socsci.ru.nl/index.php/123456?lang=en]'') or by referring to the main survey page ''[http://survey.socsci.ru.nl questions.socsci.ru.nl]''. Note that in the latter case the participant has to find the survey in a list. By default surveys are not listed on the main page. Change this in the ''survey settings'' if you wish. The preferred way is using direct links.

There is no limit on the number of surveys that you can make or the number of participants in a survey.

== Tutorial ==
There is a [https://www.socsci.ru.nl/wilberth/limesurvey/01intro.html Limesurvey beginner tutorial] for use of Limesurvey on the Radboud University Faculty of Social Sciences.

== Callaboration ==
To work with multiple people on the same survey, follow the instructions on our [[Help:LimeSurvey/Collaboration|Collaboration]] page.

== Template ==
The TSG has helped to create a Radboud-branded template for Limesurvey. When creating a new survey, it should be applied by default. If not, go to: 
Survey properties -> General settings -> Presentation & navigation -> Template -> Radboud -> Save 
[[File:Limesurvey_theme.png|thumb|none|480px|Select Radboud Template]]

 
'''Note:''' The Radboud template does not yet feature a fully responsive design and may therefore not be suitable for use on mobile devices or small screens.

== Sona integration ==
If you want to use Sona to invite people to take your survey, please follow the [http://www.sona-systems.com/help/limesurvey.aspx manual provided bij Sona]. Furthermore, if this participant ID should be stored in LimeSurvey such that it is possible to link a response to a participant ID, then you would also have to follow the instructions in the [https://manual.limesurvey.org/Panel_integration manual provided by LimeSurvery]. Please make sure to test whether it works with a [https://tsgdoc.socsci.ru.nl/index.php/Online_experiment_systems#Pilot_Run pilot run].

== Data Storage ==
Surveys and collected data are stored on campus. The server is not to be used for long term data storage. Surveys and data may be removed after a year without prior warning.

== Support ==
The TSG provides limited technical support for Limesurvey. Users themselves are responsible for the creation and design of their surveys, as well as the data analysis. For Help on designing your survey you can contact [mailto:p.vangroenestijn@maw.ru.nl Pieter van Groenestijn (RTOG)]. For questions about the use of Limesurvey, please consult the [http://manual.limesurvey.org/ manual] or the [https://www.limesurvey.org/community community support].
For technical support, contact our [[Administrator]] or [mailto:maarten.snellen@ru.nl Eric Lieffers] (server admin).



==External Links== 
*{{Official website|http://limesurvey.org}}
* [http://questions.socsci.ru.nl Radboud Survey]