Before data collection starts

Scanner¶

Once finalized the protocol development (before the first session of the first participant), the protocol(s) MUST be frozen and remain unchanged throughout the data collection effort.

Create the necessary protocols as described in the protocol management section.

Hardware: installation of instruments¶

Below is the overall setup of the instruments:


Stable configuration of the pyshiological and eye-tracking recording elements. Most of the recording devices are located on a rack in the access panel cupboard of the Control Room.

Install the BIOPAC¶

Set up the line frequency switches on the back of the BIOPAC amplifier depending on your country frequency to reduce noise. Both switches should be DOWN if your country's line frequency is 50Hz. Both switches should be UP if your country's line frequency line is 60Hz.
Check that the RB (DA100C) and ECG (ECG100C) channels are set to channel 1 and channel 2, respectively.
Connect the MP160, SPT100D, AMI100C, DA100C, and ECG100C together if it has not been done yet.
Plug in the Ethernet (the plug is on the back side of the BIOPAC), and leave it ready to connect the recording PC.
Ensure that the Mode switch of the MMBT-S Trigger Interface Box adapter (pink color box) is set on the P position.
Connect the micro-USB B end of a long USB-A to micro-USB B cable into the appropriate input socket of the MMBT-S Trigger Interface Box adapter (N-shaped pink-color box). Leave the USB-A open end accessible for connection to the stimuli presentation computer ███.
Connect the parallel cable to the 25-pin socket at the back of the SPT100D of the BIOPAC and to the parallel port of the MMBT-S (N-shaped pink box).

Connection of digital signals
Pass the RB's tube (AFT30-XL 10 m) through the access cylinder with the help of one person inside the Scanning Room.
Connect the RB's tube proximal end to the TSD160A's inlet marked with the minus (-) symbol.
Connect the parallel port end of the cable that comes out of the MECMRI-2 amplifier to the filter welded onto the access panel.
Inside the Scanning Room, connect the MRI-compatible cable where the ECG leads will be connected to the parallel port weld to the access panel.
Plug the power cord to the back socket of the BIOPAC and onto the multiple power socket extension.

Install the GA¶

Set the GA on the middle shelf of the rack.
Pass the RB's short tube (AFT30-L 4 m) through the access cylinder with the help of someone else at the Scanning Room end.
Connect the proximal end of the composite oxygen tube to one inlet of DM-060-24 desiccant chamber.
Connect the free inlet of the dessicant chamber to the MLA0343 drying tube.
Remove the cap of the gas input (Sample In, front panel of the GA).
Connect the MLA0110 flow valve to the gas inlet of the GA.

The MLA0110 flow valve MUST be replaced after some ten sessions.
Connect the MLA0343 drying tube to the MLA0110 flow valve.

The MLA0343 drying tube and the DM-060-24 desiccant chamber MUST be replaced when their inside color turns into pink.

Plug the power cord to the back socket of the GA and onto the multiple power socket extension.
Connect the coaxial end of one BNC-jack cable to the CO₂ output in the back of the GA and connect the other end (jack plug) into the input end of the INISO/A filter.
Connect one end (RJ-11 to RJ-11) to the output of the INISO/A filter you just installed.
Connect the other RJ-11 end into channel 3 of the AMI100C module.
Connect the coaxial end of the other BNC-jack cable to the O₂ output in the back of the GA and connect the other end (jack plug) into the input end of the INISO/A filter.
Connect one end (RJ-11 to RJ-11) to the output of the INISO/A filter you just installed.
Connect the other RJ-11 end into channel 4 of the AMI100C module.

Install the ET computer¶

Install the ET computer on the bottom shelf.
Install the screen and peripherals (keyboard, mouse) on the top shelf, and connect them to the PC.
Connect the power cord of the PC to the power multiple-socket extension.
Pass the optic fiber (orange wire) and the power cable (the one with a fabric sheet) through the access cylinder with the help of someone else inside the Scanning Room.

This operation requires two people

One person will feed the cables from the control room interface of the access cupboard. The other person will gently pull the two cables from inside. Both people will lift the cable to avoid its abrasion with the edges of the metallic cylinder, which is the passage between exterior and interior of the scanner room. Once the sliding of the cable is finished, leave the extremities inside the scanner room in the left-top corner, far from the scanner because they are magnetic.

Cleanup inside the scanning room¶

Several tubes and cables will be now hanging from the access cylinder at the Scanning Room end.

Roll these cables and tubes and store them organized in the cupboard, ready for their connection when needed.
The RB may be stored with these cables and tubes to.

Software¶

Preparing the physiology recording laptop (███)¶

Preparing the stimuli presentation laptop (███)¶

The stimuli presentation laptop and any other box you want to use for debugging and development will require a few additional software packages to be available.

Installing EyeLink (eye tracker software)¶

The EyeLink software MUST be installed BEFORE Pychopy

Log on ███ with the username ███ and password *****.
Enable Canonical's universe repository with the following command:
```
sudo add-apt-repository universe
sudo apt update
```

Install and update the ca-certificates package:

sudo apt update
sudo apt install ca-certificates

Add the SR Research Software Repository signing key:

curl -sS https://apt.sr-research.com/SRResearch_key | gpg --dearmor | sudo tee /etc/apt/trusted.gpg.d/sr-research.gpg

Add the SR Research Software Repository as an Aptitude source:

sudo add-apt-repository 'deb [arch=amd64] https://apt.sr-research.com SRResearch main'

Install the EyeLink Developers Kit:

sudo apt install eyelink-display-software

Install the EyeLink Data Viewer:
```
sudo apt install eyelink-dataviewer
```

Installing our synchronization server¶

During the session, we run a synchronization server that acts as a hub for the signals (triggers, task events, etc.) that define the experiment. For the best experience, we daemonize the synchronization service (meaning, we make it a service of the operative system that runs in the background). To install it as a service, please follow the documentation in the appendix

Locate the latest version of the synchronization service on your system. It is within the SOPs repository, at <path>/code/synchronization/forward-trigger-service.py.

Install the necessary libraries as root:

sudo python3 -m pip install -r <path>/code/synchronization/requirements.txt

Test the service is properly installed:
```
sudo python3 code/synchronization/forward-trigger-service.py --disable-mmbt-check
```
Use the --disable-mmbt-check flag only if you do not plan to connect the MMBT-S trigger box
Test operation with our test client:

Check the server's log file at /var/log/forward-trigger-service.log

Open a separate terminal on a separate window Then, open and follow the log file:
```
less +F /var/log/forward-trigger-service.log
```
Return to the original terminal, keeping the other window visible and execute:
```
python code/synchronization/forward-trigger-client.py
```
The log file should now have added two lines like:
```
2023-10-12 14:44:31.788 - INFO - Data received: <b'\x02'>
2023-10-12 14:44:31.788 - INFO - Forwarded <b'\x02'>
```

Testing the service without the MMBT-S connected

Testing the service without the MMBT-S trigger box connected requires emmulating /dev/ttyACM0:

Ensure socat and screen are installed (if not already):

sudo apt-get update
sudo apt-get install socat screen

Create a virtual serial port and establish a symbolic link to /dev/ttyACM0 using the following command:

sudo socat PTY,link=/tmp/virtual_serial_port PTY,link=/dev/ttyACM0,group-late=dialout,mode=666,b9600

With screen, listen to the new virtual serial port:
```
screen /dev/ttyACM0
```
!!! tip "Alternatively, you can check the server's log file at /var/log/forward-trigger-service.log"
Press s and verify that ^A appears in the screen terminal.

Prepare the Psychopy experiments¶

The appendix has some guides on how to install Psychopy.

Log on ███ with the username ███ and password *****.

Make sure to load the correct environment

Deactivate conda (if active):
```
conda deactivate
```
Load the new virtual environment:
```
source $HOME/psychopyenv/bin/activate
```

Fork the HCPh-fMRI-tasks repository under your user on GitHub.

Clone the HCPh-fMRI-tasks repository:

git clone git@github.com:<your-gh-username>/HCPh-fMRI-tasks.git

Set-up the original repository as upstream remote:

git remote add upstream git@github.com:theaxonlab/HCPh-fMRI-tasks.git

Open Psychopy and (optionally) a experiment file corresponding to a task by typing the following command in the terminal:
```
psychopy --no-splash -b task-qct_bold.psyexp
```
For each task, check the following:
- task-qct_bold.psyexp (quality-control task, QCT):
  - time it to confirm the length, and
  - check the task runs properly.
- task-rest_bold.psyexp (resting-state fMRI):
  - time it to confirm the length, and
  - check that the movie is played.
- task-bht_bold.psyexp (breath-holding task, BHT):
  - time it to confirm the length, and
  - check the task runs properly.
- task-fixation_dwi.psyexp (fixation point during DWI):
  - time it to confirm the length, and
  - check the task runs properly.
Check that Dropbox is operative.
Create a softlink under the tasks repository to directly store outputs into Dropbox:
```
ln -s  /data
```
For the 'reliability sample' this link was created differently.

As a result, a manual copy step was necessary to synchronize the data (see tear-down)

Prepare data management (intake and backup) with ███¶

We employ ███ as the server to automatically upload data to the backup repository (\@\:\). For the physiological recordings (acquired on ███ for BIOPAC-registered signals, and on ███ for the eye-tracking), data is synchronized into ███ via Dropbox.

Create a softlink pointing to the BIOPAC data:

ln -s  /data/datasets/hcph-pilot-sourcedata/recordings/BIOPAC

Create a softlink pointing to the eye-tracking data:

ln -s  /data/datasets/hcph-pilot-sourcedata/recordings/psychopy

Setup a cron job to execute automatically the synchronization:

crontab -e
[ within your file editor add the following line ]
0 2 * * * rsync -avurP /data/datasets/hcph-pilot-sourcedata* <user>@<host>:<path>/sourcedata-pilot &> $HOME/var/log/data-curnagl.log

Calibration of the GA¶

The AcqKnowledge software must be re-calibrated every two months, approximately.

A gas mixture bottle with a known CO₂ and O₂ concentrations is necessary

CO₂ concentration must be between 5% and 10%, while O₂ within 5% and 21%. A second reference mixture is necessary, and room air can be used, knowing that atmospheric contents by volume are 0.039 ±0.001% for CO₂ and 20.946 ±0.003% for O₂.

Connect the BIOPAC to the Physiology recording laptop (███) as described in this section.
Connect the AcqKnowledge License Key into a USB Port of the Physiology recording laptop (███).
Open AcqKnowledge software on the Physiology recording laptop (███).
Open the template graph file (EXP_BASE.gtl)
Edit the configuration of the inputs 3 (connected to the CO₂ output of the GA) and 4 (connected to the O₂ output of the GA). Lower and upper calibration points can be set by sampling the input a number of times with the AcqKnowledge utility.
Overwrite the template graph file EXP_BASE.gtl.