ReproStim is a video capture and recording suite for neuroimaging and psychology experiments. Its goal is to provide experimenters with a complete record of audio and visual stimulation for every data collection session by making it possible to easily collect high fidelity copies of the actual stimuli shown to each subject in the form of video files that can be stored alongside behavioral or neuroimaging data in public repositories.
ReproStim provides for enhanced experimental reproducibility and a safeguard against data loss in cases of data-collection irregularites. Because ReproStim provides an exact record of the actual stimuli delivered during any given experimental session, it makes it possible to precisely reproduce experimental sessions, even if the original trial sets were randomized and precise trial details not recorded. In cases of experimental irregularities, such as aborted fMRI runs, unexpected glitches in trial timing, or programming errors that cause records of trial conditions to be lost, valuable data (which can be especially costly in cases of fMRI of ECog, for example) can be recoded and recovered using the audio-visual record provided by ReproStim.
ReproStim requires minimal effort on behalf of investigators. Once it is setup as the default mode within a behavioral lab or neuroimaging center, investigators can reap the benefits of ReproStim without any additional effort on the part of invidiual experimenters. When successfully set up, ReproStim runs in the background, silently collecting, cataloging, and storing all audio and visual stimulation delivered to experimental subjects.
Before using ReproStim you will need a minimum of the the following components:
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Magewell USB Capture Plus device (MWC)
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Stimulus control computer (SC) with A/V out to presentation device
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External presentation device (EPD)
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Video capture computer (VC) with USB-C port
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Supporting cables including A/V splitter cables
Given a stimulus presentation computer (SP) that controls the content and flow of the experimental presentation and presents A/V to experimental subject on external monitor or projector (EPD), the setup without ReproStim would be something like:
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Schematic A.
------ ------- | SC | -- A/V Out --> | EPD | ------ -------With the addition of ReprosStim, the setup will look like this:
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Schematic B.
------ ------- | SC | -- A/V Out --> A/V Splitter --> | EPD | ------ | ------- V ------- ------ | MWC | -- USB-C --> | VC | ------- ------
Most experimental setups include something like Schematic A, with a stimulus control computer (SC) that sends A/V information to the experimental subject. For example, in the Dartmouth Brain Imaging Center (DBIC), experimenters can use their own laptop or a dedicated computer in the scan control room for SC. The External Presentation Device for video (EPDv) in the DBIC MRI suite is a projector that projects through the wall of the shielded scan room to a rear-projection screen located at the back of the MRI scanner bore; and the EPDa (audio) comprises MRI-safe headphones worn on the subject's head.
The A/V out connections from SC can be any standard as long as you have the appropriate adapters, dongles, etc. However, if your Video out does not support embedded audio (e.g. VGA), then you will need a separate audio out set of splitters and cables. The Magewell device has standard audio ports to accomodate this eventuality.
Note: Missing from Schematics A and B, is any connection back to SC that records subject response information. That's because ReproStim is not interested in how the subject responds. If you like, imagine arrows pointing from EPD to a "subject" node, and then more arrows pointing from the subject node to some response input device (RID?) and back to SC for recording... ReproStim will not interfere.
The current version of ReproStim has only been developed and tested for the Magewell USB Capture DVI Plus device (MWC) . However, we anticipate that it will be relatively painless to support at least all devices in the USB Capture Plus Family. Information about these devices and supporting software can all be found at www.magewell.com
The video capture computer (VC) does most of the work for ReproStim. The software running on this computer runs as a service that is always on as long as the computer is running, which is all the time. Therefore I will refer to VC also as the ReproStim server. In a nutshell, the server software monitors the video signal coming from SC into MWC. If there is any video coming over the connection, it gets recorded for posterity.
Current development of ReproStim, including our working setup at the DBIC, uses a Linux box running Debian Linux. We anticipate that any Nix/Mac setup running on a modern desktop will be amply sufficient as a ReproStim Server, and should be relatively painless to configure.
The current DBIC computer is a small-profile desktop that resides in the control of the scan suite, quietly recording all video presented to all subjects.
On Debian
apt-get install -y ffmpeg libudev-dev libasound-dev libv4l-dev libyaml-cpp-dev libspdlog-dev catch2 v4l-utils libopencv-dev libcurl4-openssl-dev nlohmann-json3-dev cmake g++
"Parsing/parse_wQR.py" script requires in zbar to be installed as well:
apt-get install -y libzbar0
cd Capture
mkdir build
cd build
cmake ..
make
Contains all code needed for setting up video capture. This includes C++ code for interfacing with the video capture device, and scheme for setting up a video-capture "server", along with helper utilities.
Contains utilities for embedding QR codes in experimental stimulus-delivery programs, such as PsychoPy, or PsychToolbox scripts.
Contains code needed for segmenting videos to include just the parts of the videos that are demarcated by embedded QR codes marking the beginning and end of experimental runs. There are also helper tools for identifying experimental runs and matching them to the parent experimental paradigm and neuroimaging data acquisitions.
VideoCapture utility internally uses Magewell Capture SDK and to make it working properly should be executed under "root" account or in case of other account - special "udev" rules should be applied there. Program will produce following error when executed in environment without proper ownership and permissions for informational purposes:
ERROR[003]: Access or permissions issue. Please check /etc/udev/rules.d/ configuration and docs.
For more information refer to item #14 from Magewell FAQ on https://www.magewell.com/kb/detail/010020005/All :
14. Can the example codes associated with USB Capture (Plus) devices in SDKv3 work
without root authority (sudo) on Linux?
Yes. Click here to download the file "189-usbdev.rules" (http://www.magewell.com/files/sdk/189-usbdev.zip) ,
move it to the directory "/etc/udev/rules.d", and then restart your computer.
NOTE: Also make sure that no other processes like ffmpeg, vlc, etc are using this video device, as it can accidentally produce the same error message ERROR[003].
This is optional step, only for information purposes:
lsusb
And locate line with device, e.g.:
Bus 004 Device 012: ID 2935:0008 Magewell USB Capture DVI+
In this sample, 2935 is the "Vendor ID", and 0008 is the "Product ID".
Optionally Magewell device name and serial number can be quickly checked with this command:
lsusb -d 2935: -v | grep -E 'iSerial|iProduct'
Create text file under "/etc/udev/rules.d/189-reprostim.rules" location with appropriate content depending on system type.
For an active/desktop user logged in via session manager it should be like:
ACTION=="add", SUBSYSTEM=="usb", ATTR{idVendor}=="2935", TAG+="uaccess"
For a daemon configuration we should provide explicit permissions like:
SUBSYSTEM=="usb", ATTR{idVendor}=="2935", MODE="0660", OWNER="reprostim", GROUP="plugdev"
Note: we can see that "ATTR{idVendor}" value 2935 is equal to one we got in step 1) from lsusb utility.
Also sample udev rules configuration added to project under "Capture/etc/udev/189-reprostim.rules" location.
Note: make sure the file has owner "root", group "root" and 644 permissions:
ls -l /etc/udev/rules.d/189*
-rw-r--r-- 1 root root 72 ... /etc/udev/rules.d/189-reprostim.rules
Make sure the user running VideoCapture utility is a member of the "plugdev" group, e.g.:
sudo usermod -aG plugdev TODO_user
Restart computer to make changes effect.
Note: we tested "sudo udevadm control --reload-rules" command without OS restart, but somehow it didn't help, and complete restart was necessary anyway.
- Build (per above) and install in the PATH
- TODO: cron job
- TODO: add user/group
- ...
- Parsing/repro-vidsort script (has hardcoded paths) sorts from
incoming/to folders per DICOM accession