From 0e0d390931ba13b96374a14cf8ea495f782eda85 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Mon, 28 Aug 2023 14:30:32 +0200 Subject: [PATCH 1/2] enh: large overhaul, including initial flowchart of the experiment --- docs/data-collection/participant-prep.md | 33 ++- docs/data-collection/pre-session.md | 45 ++- docs/data-collection/preliminary.md | 358 +++++++++++++---------- docs/data-collection/scanning.md | 154 +++++----- docs/data-collection/tear-down.md | 17 +- docs/stylesheets/extra.css | 18 ++ mkdocs.yml | 9 +- 7 files changed, 382 insertions(+), 252 deletions(-) diff --git a/docs/data-collection/participant-prep.md b/docs/data-collection/participant-prep.md index 608f58b7..3dd38e3c 100644 --- a/docs/data-collection/participant-prep.md +++ b/docs/data-collection/participant-prep.md @@ -29,12 +29,13 @@ - [ ] Accompany them to the bathroom (situated at {{ secrets.rooms.bathroom | default("███") }}), and ask whether there is anything else they anticipate they will need. - [ ] If the test is positive, the person **CANNOT PARTICIPATE** in the study. You MUST be understanding of the situation as most likely the person will not be aware of the circumstance. -- [ ] Tell the participant they will be holding an alarm button throughout the session, and that they may use it any time whenever they need to stop the experiment. +- [ ] Instruct the participant on how to use the alarm button: - > During the duration of the exam, you'll have an alarm button on your hand. - > You can use it at any moment. - > We will first talk with you to check everything is fine, and we will stop the session whenever you need to stop the experiment. - > There is no need for you to endure uncomfortable experiences or anxiety (for instance, if you feel claustrophobic) + ???+ quote "Alarm button should be used when needed" + During the duration of the exam, you'll have an alarm button on your hand. + You can use it at any moment. + We will first talk with you to check everything is fine, and we will stop the session whenever you need to stop the experiment. + There is no need for you to endure uncomfortable experiences or anxiety (for instance, if you feel claustrophobic) ### Describing the development of the session - [ ] Describe the participant how the session will develop, with special attention to tasks. In the first session, show the task while explaining them for clarity. Let them interrupt you to ask for clarifications and answer all the questions that may arise. @@ -116,13 +117,21 @@ Is everything clear to you? Do you have any questions? ### Finalizing the preparation -- [ ] Indicate the participant where the door to the changing room is if changing into scrubs is necessary. Otherwise, offer them a box to deposit everything they have in their pockets and all jewelry/hair accessories. +- [ ] Offer the participant a box to deposit everything they have in their pockets and all jewelry/hair accessories, and indicate the clothing to enter the scanning room: - > Before we continute, we need to make sure we do not introduce any dangerous object in the magnet room. - > - > [IF THEY NEED TO CHANGE INTO SCRUBS] Here you will find a changing room, I have prepared some scrubs for you. Please remove all your clothes and leave them in the changing room. Please keep your underwear on (if a woman, double check that **their undergarment DOES NOT contain any large metallic part** such as shaping guides, and request their removal if they do). - > - > [IF THEY CAN WEAR THEIR CLOTHES] Please deposit here all your belongings, your belt, your glasses, your jewelry and any accessories, piercings, etc. that you have on you. + ??? quote "*Dress code* inside the scanner **if they need to CHANGE INTO SCRUBS**" + Before we continute, we need to make sure we do not introduce any dangerous object in the magnet room. + + Here you will find a changing room [SHOW THEM THE CHANGING ROOM]. + I have prepared some scrubs for you. + Please remove all your clothes and leave them in the changing room. + Please keep your underwear on [if a woman, ask whether **their undergarment DOES NOT contain any large metallic part** such as shaping guides, and request their removal if they do]. + + ???+ quote "*Dress code* inside the scanner **if they CAN WEAR THEIR CLOTHES**" + Before we continute, we need to make sure we do not introduce any dangerous object in the magnet room. + + Please deposit here all your belongings, your belt, your glasses, your jewelry and any accessories, piercings, etc. that you have on you. + If a woman, ask whether **their undergarment DOES NOT contain any large metallic part** such as shaping guides, and request their removal in the changing room. - [ ] Help the participant to prepare their skin and place the ECG electrodes: @@ -168,7 +177,7 @@ ## Installing the participant in the SCANNING ROOM -??? info "Thanks to Stephanie Bogaert, MSc, Pieter Vandemaele, MSc and Pim Pullens, PhD" +??? thanks "Thanks to Stephanie Bogaert, MSc, Pieter Vandemaele, MSc and Pim Pullens, PhD" Some of the pictures in this section have been extracted from the [Ghent Institute for functional and Metabolic Imaging MRI User 2019](http://gifmi.ugent.be/drupal/system/files/documents/GIfMI_MRI%20user%20manual_BASIC_SiemensPrisma_EN.pdf) written by Stephanie Bogaert, MSc, Pieter Vandemaele, MSc and Pim Pullens, PhD. We express our gratitude that they put together such a comprehensive guide. - [ ] Have the participant remove their shoes at the entrance of the scanning room. diff --git a/docs/data-collection/pre-session.md b/docs/data-collection/pre-session.md index 56cb1c53..19a8e47e 100644 --- a/docs/data-collection/pre-session.md +++ b/docs/data-collection/pre-session.md @@ -1,8 +1,42 @@ +Instructions of operations to be performed before the participant arrival, **before EACH session** (i.e., DAY OF SCAN) -!!! info "Thanks" - All the documentation about the eye-tracker is derived from Benedetta Franceschiello's user guide. We greatly appreciate her help with the eye-tracker. -Instructions of operations to be performed before the participant arrival, **before EACH session** (i.e., DAY OF SCAN) +## Three days BEFORE THE FIRST SESSION + +- [ ] Verify that as part of the [recruitement and screening procedure](../recruitment-scheduling-screening/recruitment.md), you have sent a copy of the MRI Safety and screening form ([EN](../assets/files/safety_form_EN.pdf)|[FR](../assets/files/safety_form_FR.pdf)) to the participant over email and confirm reception by checking the 'First contact email sent' column in [our recruits spreadsheet]({{ secrets.data.recruits_url | default("/redacted.html") }}). +- [ ] Verify also that you confirmed that the participant has read and understood the document, and in particular, you double-checked that they do not have any MRI contraindications, by checking the 'Phone interview done' and 'Participant volunteer and eligible' column in [our recruits spreadsheet]({{ secrets.data.recruits_url | default("/redacted.html") }}). +- [ ] If the phone call interview was more than three days before the first session, call the participant again to reconfirm the following information: + - [ ] Remind the participant that any jewelry should be removed prior to the scan. + - [ ] Indicate that they MUST shave the upper area of their chest where the ECG electrodes will be placed, if there is hair. The ECG electrodes MUST directly contact the skin. + - [ ] Confirm clothing: + - [ ] if allowed to wear street clothes, remind the participant to avoid clothing with metal or that would uncomfortable to lie in for the duration of the scan; otherwise + - [ ] remark the participant they will be given a gown and they will need to change before every session. + - [ ] Repeat at what time and where will you meet the participant. + - [ ] Verify that the participant has your phone number {{ secrets.phones.study | default("███") }} to call you in case he gets lost. + - [ ] **FEMALE PARTICIPANTS ONLY**: Remind the participant that pregnant women cannot undergo our MRI protocols. Therefore, they will take a pregnancy test (which we will have prepared) before the first session. +- [ ] If participant has indicated nervousness or history of claustrophobia, organize a session to use the mock scanner. + +## BEFORE DAY OF SCAN + +- [ ] Print [the informed consent form](../assets/files/icf_FR.pdf) (**first session only**), an MRI safety screener ([EN](../assets/files/safety_form_EN.pdf)|[FR](../assets/files/safety_form_FR.pdf)) and a receipt form for each participant that will get scanned. +- [ ] Make sure you have internet access, and update the [HCPh-fMRI-tasks repository](https://github.com/TheAxonLab/HCPh-fMRI-tasks) on *{{ secrets.hosts.psychopy | default("███") }}*: + ``` + git fetch upstream + git checkout main + git rebase upstream/main + ``` +- [ ] On the *{{ secrets.hosts.psychopy | default("███") }}* laptop, open a terminal and execute `conda deactivate`. +- [ ] Open psychopy 3 by typing `psychopy` +- [ ] Load in the different experiments and check for proper functioning: + - [ ] {{ settings.psychopy.tasks.func_rest }} (resting-state fMRI): + - [ ] time it to [confirm the length](preliminary.md#task-timing), and + - [ ] check that the movie is played. + - [ ] {{ settings.psychopy.tasks.func_bht }} (breath-holding task, BHT): + - [ ] time it to [confirm the length](preliminary.md#task-timing), and + - [ ] check that the movie is played. + - [ ] {{ settings.psychopy.tasks.func_pct }} (positive-control task, PCT): + - [ ] time it to [confirm the length](preliminary.md#task-timing), and + - [ ] check that the movie is played. ## Documentation and other non-experimental devices @@ -136,6 +170,11 @@ Instructions of operations to be performed before the participant arrival, **bef ## Setting up the ET arm +??? thanks "Thanks to Benedetta Franceschiello!" + + All the documentation about the ET is derived from Benedetta Franceschiello's user guide. + We greatly appreciate her help with the device. + - [ ] Go to room {{ secrets.rooms.et_camera | default("███") }} and bring the blue box labeled *Eye-Tracker only for fMRI* into the scanning room. This box contains the ET arm with the camera and infrared lamp mounted on it, lenses, and the special infrared mirror. The box should be found in the first cabinet on the left section of the cupboard. diff --git a/docs/data-collection/preliminary.md b/docs/data-collection/preliminary.md index b4f94093..043df515 100644 --- a/docs/data-collection/preliminary.md +++ b/docs/data-collection/preliminary.md @@ -1,16 +1,128 @@ +## Overall experimental setting + +The goal of the experimental setting is to obtain several functional MRI tasks and a long diffusion MRI scan with synchronized physiological recordings, including gas contents with a gas analyzer (GA), eye tracking (ET; including the right eye position, pupil size, blinks, etc.), respiration tracking through a pneumatic respiration belt (RB), and finally MRI-compatible electrocardiogram (ECG). + +The overall experimental setting can be sumarized as follows: + +``` mermaid +flowchart TB + + subgraph "Scanning Room" + direction TB + sr1[Scanner] + sr2[Cannula] + sr3[RB] + sr4[ECG] + sr5[ET] + end + + subgraph "BIOPAC" + direction TB + biopac1[DA100C] + biopac2[ECG100C MRI] + biopac3[AMI100D] + biopac4[STP100D] + end + + sr1 --->|Trigger| sb[Syncbox] + sr2 ---> ga[Gas Analyzer] + sr3 --->|"Negative (-)"| biopac1[DA100C] + sr4 ---> biopac2[ECG100C MRI] + sr5 ---> et[Eye Tracker PC] + + ga --->|"Channel 3 (CO2)"| biopac3 + ga --->|"Channel 4 (O2)"| biopac3 + + sb --->|USB| pc1["Stimuli presentation Laptop ({{ secrets.hosts.psychopy | default("███") }})"] + pc1 <--->|Ethernet| et + pc1 --->|USB| modem[MMBT-S Interface] + pc1 --->|HDMI| display[Proyector] + modem --->|25-pin parallel| biopac4 + + BIOPAC --->|Ethernet| pc2["Physio-recording Laptop ({{ secrets.hosts.acqknowledge | default("███") }})"] +``` + +The above graph can be broken down as follows: + +1. **Signals generating from the Scanning Room**. + In addition to the MR imagery produced by the scanner, the participant will be wearing the RB, the ECG leads, a nasal cannula to retrieve the expired gases, and finally their right eye will be recorded with the infrared camera of the ET. + All those probes and devices carry signals outside the Scanning Room either through cables or tubes, with the access panel as the interface. + The access panel also has a connector carrying the **trigger** signals generated by MR schemes, which indicate important events in the MRI acquisition (typically, one trigger pulse is generated for each new *repetition time* —TR—, e.g., with every fMRI volume). +1. **Syncbox**. + A *NordicLabs Syncbox* receives TTL (transistor-transistor logic) triggers from the scanner. + This box can just forward the triggers converted into other formats and/or manipulate them (e.g., filter, generate, etc.). +1. **Gas analyzer (GA)**. + The GA is a device that continuously measures the amount of two gases (CO2 and O2) from a sample fed at the front of the device with a connected tube (this tube comes from inside of the Scanning Room and ends in the nasal cannula the participant is wearing, as shown in the graph). +1. **BIOPAC**. + The BIOPAC is the main recording hub. + It directly receives analogical signals from the Scanning Room (for the case of the RB and the ECG). + Indirectly, it receives the analogical signal from the GA, and digital signals from the *Psychopy laptop* ({{ secrets.hosts.psychopy | default("███") }}). + +1. **Eye tracker (ET)**. + The ET is composed of two main elements: + (i) inside the scanner's bore, we place an arm that holds an infrared lens and camera sensor on one side and an infrared lamp that illuminates the right eye of the subject through a special mirror to reflect the infrared spectrum; and (ii) a PC tower that receives the camera recordings, postprocess the images and calculates the final parameters of interest (position of the eye, pupil size, etc.). + The ET is also connected to the *Psychopy laptop* ({{ secrets.hosts.psychopy | default("███") }}), and communicates bi-directionally with it (e.g., to record logs or receive "messages" such as triggers or task events). + The ET **is NOT connected to the BIOPAC**, with the implication that the ET data is not stored with the other physiological information. +1. **Stimuli presentation laptop**. + The *Psychopy laptop* ({{ secrets.hosts.psychopy | default("███") }}) has the *Psychopy* software install and with it, the task programs are executed. + This experiment consists of three tasks: breath-holding task (*BHT*), resting-state fMRI (*rest*), and a positive-control task (*PCT*). + This laptop also stores the data recorded by the ET at the end of the experiment. +1. **Physiology recording laptop**. + The *AcqKnowledge laptop* ({{ secrets.hosts.acqknowledge | default("███") }}) runs the BIOPAC's *AcqKnowledge* software and with it, this computer records the signals and allows visualization of the data coming from the BIOPAC. + All the inputs to the BIOPAC are multiplexed through into an Ethernet cable that is connected to this laptop. + ## Once, at the beginning of the project -!!! important "Emergency procedures" +### Setting up the scanner protocol at the MR console + +!!! warning "Emergency procedures" It is critical you fully understand and study the [emergency procedures to run an MRI scan at CHUV](./emergency-procedures.md). -### Install the gas analyzer (GA) +!!! important "Follow Reproin conventions" -- [ ] Watch the gas analyzer (GA) video: - + When assigning names to the MR sequences in the protocol, make sure to follow the [Reproin conventions](https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html) to maximally facilitate the conversion into BIDS. + + +Once the protocol is decided upon, and after any updates, make sure of storing the protocol. + +!!! warning "Login as an advanced user to save protocol" + As a good practice, always work as the standard user `{{ secrets.login.username_scanner | default("janedoe") }}`. + Change for *advanced user mode* if you want to save the protocol. + + - [ ] Simultaneously press the Tab + Delete + [→ on the control-computer's keyboard: + + > Username: `{{ secrets.login.superusername_scanner | default("superjanedoe") }}` + > + > Password: `{{ secrets.login.superuserpass_scanner | default("******") }}` + + !!! Danger "After three wrong password entries, access will be denied, and only a Siemens engineer will be able to unlock the MR scanner." + +- [ ] Update the *Number of measurements* in all `func-bold_task-*` sequences, according to the [previously recorded timings](#task-timing): + + $$N_\text{measurements} = L_t / \text{TR}, \quad t \in \{\text{bht}, \text{pct}, \text{rest}\},$$ + + where $L_t$ is the length of a particular task $t$ (either BHT, PCT, or resting state) in seconds as timed before, and + $\text{TR}$ is the **repetition time** of the BOLD sequence, in seconds. + +- [ ] Now that you are logged in as an advanced user, save your protocol: + - [ ] Open the Dot-Cockpit window + ![](../assets/images/save_protocol1.jpg) + - [ ] In `Browse`, find the right folder to save the protocol in (*RESEARCH* ⤷ *Oscar*). + - [ ] Right click on the folder and select *New* ⤷ *Program*. This opens an empty page in the program editor + ![](../assets/images/save_protocol2.jpg) + ![](../assets/images/save_protocol3.jpg) + - [ ] Select all the sequences you want to run from the sequence list and click right to copy. + ![](../assets/images/save_protocol4.jpg) + - [ ] Drag or paste the copied sequences in the program editor. + ![](../assets/images/save_protocol5.jpg) + - [ ] Once finished, click on the floppy disk icon (🖫) in the upper left to save. + - [ ] Give the protocol a relevant name starting with the date of acquisition in the format YYYYMMDD and click Save. + ![](../assets/images/save_protocol6.jpg) + - [ ] If desired, the protocol details can also be downloaded as a pdf on a peripherical USB key. + - [ ] Right-click on the protocol and select *Print* + - [ ] Save the PDF in your USB key. +- [ ] Make sure you save a different protocol for each of the four PE directions (i.e., AP, PA, LR, RL). ### Install the BIOPAC @@ -24,7 +136,7 @@ - [ ] Get familiar with the BIOPAC system: - [ ] We use the BIOPAC to synchronize and output in a single file all the physiological recordings: cardiac pulsation, respiration and CO2 concentration. ![Biopac_setup](../assets/images/Biopac_setup.jpg "BIOPAC front side") - - [ ] The AMI100C unit can receive up to 16 analog signals. + - [ ] The AMI100C unit can receive up to 16 analog signals. - [ ] The DA100C unit records the signal coming from the respiration belt. Plug the TSD160A unit on the DA100C. - [ ] The ECG100C MRI unit records the electrical signal coming from the heart via the ECG. Plug the MECMRI-2 unit on the ECG100C unit. - [ ] The [SPT100D (solid state relay driver unit)](../assets/files/STP100D.pdf) is used to input digital signals that must be recorded (e.g., the trigger signals from the scanner) @@ -60,76 +172,20 @@ - [ ] Configure whether you want to collect directly to hard disk and autosave settings - [ ] Save the experiment, making sure you choose a "graph template file" (with extension `.gtl`) -### Setting up the Connection between the Biopac and the Psychopy Laptop: - -!!! important "It's fundamental to have a reliable means of communication with the BIOPAC digital inputs" - - The following guidelines set up a little service on a linux box that keeps listening for key presses (mainly, the s trigger from the trigger box), and RPC (remote procedure calls) from typically *Psychopy* or similar software. - - The service is spun up automatically when you connect the MMBT-S modem interface that communicates with the BIOPAC (that is, the *N-shaped pink box*) - -- [ ] Copy the [latest version of the code to send triggers](https://github.com/TheAxonLab/hcph-sops/blob/mkdocs/code/synchronization/forward-trigger-service.py) -- [ ] To automatically start the program when the BIOPAC is connected, create a udev rule as follows: - ``` - sudo nano /etc/udev/rules.d/99-forward-trigger.rules - ``` -- [ ] Add the following rule to the file: - ``` - ACTION=="add", KERNEL=="ttyACM0", SUBSYSTEM=="tty", TAG+="systemd", ENV{SYSTEMD_WANTS}="forward-trigger.service" - ``` -- [ ] Save the file and exit the editor. -- [ ] Run the following command to reload the udev rules: - ``` - sudo udevadm control --reload-rules - ``` -- [ ] Create a systemd service unit file: - ``` - sudo nano /etc/systemd/system/forward-trigger.service - ``` -- [ ] Add the following content to the file (Adapt the path to forward-trigger.py to the location on your computer): - ``` - [Unit] - Description=Forward Trigger Service - After=network.target +### Install the gas analyzer (GA) - [Service] - ExecStart=/usr/bin/python3 /path/to/forward-trigger.py - WorkingDirectory=/path/to/forward-trigger/directory - StandardOutput=null +- [ ] Get familiar with the [GA's manual](../assets/files/GA_manual.pdf) and watch the following video: + - [Install] - WantedBy=multi-user.target - ``` -- [ ] Save the file and exit the text editor. -- [ ] Run the following command to enable the service to start at boot: - ``` - sudo systemctl enable forward-trigger - ``` -- [ ] Run the following command to reload the systemd daemon: - ``` - sudo systemctl daemon-reload - ``` +### Preparing the *Stimuli presentation laptop* ({{ secrets.hosts.psychopy | default("███") }}) -### Verifying Trigger Transfer Without BIOPAC Connection: -- [ ] 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 - ``` -- [ ] Press s and verify that `^A` appears in the screen terminal. +This block describes how to prepare a laptop with a running *Psychopy 3* installation, the *EyeLink* software corresponding to the Eye Tracker, and finally an *Experiment synchronization service*. -### Stimuli presentation: *psychopy* +#### Stimuli presentation with *psychopy* -- [ ] Prepare a laptop with a running Psychopy 3 installation AND the EyeTracker software. - For these SOPs, the designated laptop for the experiments is *{{ secrets.hosts.psychopy | default("███") }}*. - [ ] [Fork the HCPh-fMRI-tasks repository](https://github.com/TheAxonLab/HCPh-fMRI-tasks/fork) under your user on GitHub. - [ ] Clone the [HCPh-fMRI-tasks repository](https://github.com/TheAxonLab/HCPh-fMRI-tasks): ``` @@ -181,11 +237,11 @@ The lengths of the three runs should be: - * {{ settings.psychopy.tasks.func_rest }} ➜ **{{ settings.mri.timings.func_rest }}**, - * {{ settings.psychopy.tasks.func_bht }} ➜ **{{ settings.mri.timings.func_bht }}**, and + * {{ settings.psychopy.tasks.func_bht }} ➜ **{{ settings.mri.timings.func_bht }}**, + * {{ settings.psychopy.tasks.func_rest }} ➜ **{{ settings.mri.timings.func_rest }}**, and * {{ settings.psychopy.tasks.func_pct }} ➜ **{{ settings.mri.timings.func_pct }}**. -### Eye-tracker: *EyeLink Software* installation +#### Installing *EyeLink* (eye tracker software) - [ ] Log on *{{ secrets.hosts.psychopy | default("███") }}* with the username *{{ secrets.login.username_hos68752 | default("███") }}* and password *{{ secrets.login.password_hos68752 | default("███") }}*. @@ -212,96 +268,88 @@ sudo apt install eyelink-dataviewer ``` -### Setting up the scanner protocol at the MR console - -!!!warning "Important: follow Reproin conventions" - - When assigning names to the MR sequences in the protocol, make sure to follow the [Reproin conventions](https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html) to maximally facilitate the conversion into BIDS. - +#### Setting up a synchronization service -Once the protocol is decided upon, and after any updates, make sure of storing the protocol. +!!! important "It's fundamental to have a reliable means of communication with the BIOPAC digital inputs" -!!! warning "Login as an advanced user to save protocol" - As a good practice, always work as the standard user `{{ secrets.login.username_scanner | default("janedoe") }}`. - Change for *advanced user mode* if you want to save the protocol. + The following guidelines set up a little service on a linux box that keeps listening for key presses (mainly, the s trigger from the trigger box), and RPC (remote procedure calls) from typically *Psychopy* or similar software. - - [ ] Simultaneously press the Tab + Delete + [→ on the control-computer's keyboard: - - > Username: `{{ secrets.login.superusername_scanner | default("superjanedoe") }}` - > - > Password: `{{ secrets.login.superuserpass_scanner | default("******") }}` + The service is spun up automatically when you connect the MMBT-S modem interface that communicates with the BIOPAC (that is, the *N-shaped pink box*) - !!! Danger "After three wrong password entries, access will be denied, and only a Siemens engineer will be able to unlock the MR scanner." +- [ ] Copy the [latest version of the code to send triggers](https://github.com/TheAxonLab/hcph-sops/blob/mkdocs/code/synchronization/forward-trigger-service.py) +- [ ] To automatically start the program when the BIOPAC is connected, create a udev rule as follows: + ``` + sudo nano /etc/udev/rules.d/99-forward-trigger.rules + ``` +- [ ] Add the following rule to the file: + ``` + ACTION=="add", KERNEL=="ttyACM0", SUBSYSTEM=="tty", TAG+="systemd", ENV{SYSTEMD_WANTS}="forward-trigger.service" + ``` +- [ ] Save the file and exit the editor. +- [ ] Run the following command to reload the udev rules: + ``` + sudo udevadm control --reload-rules + ``` +- [ ] Create a systemd service unit file: + ``` + sudo nano /etc/systemd/system/forward-trigger.service + ``` +- [ ] Add the following content to the file (Adapt the path to forward-trigger.py to the location on your computer): + ``` + [Unit] + Description=Forward Trigger Service + After=network.target -- [ ] Update the *Number of measurements* in all `func-bold_task-*` sequences, according to the [previously recorded timings](#task-timing): + [Service] + ExecStart=/usr/bin/python3 /path/to/forward-trigger.py + WorkingDirectory=/path/to/forward-trigger/directory + StandardOutput=null - $$N_\text{measurements} = L_t / \text{TR}, \quad t \in \{\text{bht}, \text{pct}, \text{rest}\},$$ + [Install] + WantedBy=multi-user.target + ``` +- [ ] Save the file and exit the text editor. +- [ ] Run the following command to enable the service to start at boot: + ``` + sudo systemctl enable forward-trigger + ``` +- [ ] Run the following command to reload the systemd daemon: + ``` + sudo systemctl daemon-reload + ``` - where $L_t$ is the length of a particular task $t$ (either BHT, PCT, or resting state) in seconds as timed before, and - $\text{TR}$ is the **repetition time** of the BOLD sequence, in seconds. +??? important "Testing the service without the syncbox connected" -- [ ] Now that you are logged in as an advanced user, save your protocol: - - [ ] Open the Dot-Cockpit window - ![](../assets/images/save_protocol1.jpg) - - [ ] In `Browse`, find the right folder to save the protocol in (*RESEARCH* ⤷ *Oscar*). - - [ ] Right click on the folder and select *New* ⤷ *Program*. This opens an empty page in the program editor - ![](../assets/images/save_protocol2.jpg) - ![](../assets/images/save_protocol3.jpg) - - [ ] Select all the sequences you want to run from the sequence list and click right to copy. - ![](../assets/images/save_protocol4.jpg) - - [ ] Drag or paste the copied sequences in the program editor. - ![](../assets/images/save_protocol5.jpg) - - [ ] Once finished, click on the floppy disk icon (🖫) in the upper left to save. - - [ ] Give the protocol a relevant name starting with the date of acquisition in the format YYYYMMDD and click Save. - ![](../assets/images/save_protocol6.jpg) - - [ ] If desired, the protocol details can also be downloaded as a pdf on a peripherical USB key. - - [ ] Right-click on the protocol and select *Print* - - [ ] Save the PDF in your USB key. -- [ ] Make sure you save a different protocol for each of the four PE directions (i.e., AP, PA, LR, RL). + - [ ] 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 + ``` + - [ ] Press s and verify that `^A` appears in the screen terminal. ## Every two months ### Calibrate the GA -- [ ] Get a gas bottle with a known CO2 concentration between 5% and 10%. -- [ ] Connect the GA to the BIOPAC as described below and start recording signal. -- [ ] In the *AcqKnoledge* software, edit the configuration of the inputs, making sure you update the voltage range for input 3 (the GA), estimated as described in [the GA's manual](../assets/files/GA_manual.pdf) -- [ ] Update the template *graph file* ([`EXP_BASE.gtl`](../assets/files/EXP_BASE.gtl)) with the calibrated input. - -## Three days BEFORE THE FIRST SESSION - -- [ ] Verify that as part of the [recruitement and screening procedure](../recruitment-scheduling-screening/recruitment.md), you have sent a copy of the MRI Safety and screening form ([EN](../assets/files/safety_form_EN.pdf)|[FR](../assets/files/safety_form_FR.pdf)) to the participant over email and confirm reception by checking the 'First contact email sent' column in [our recruits spreadsheet]({{ secrets.data.recruits_url | default("/redacted.html") }}). -- [ ] Verify also that you confirmed that the participant has read and understood the document, and in particular, you double-checked that they do not have any MRI contraindications, by checking the 'Phone interview done' and 'Participant volunteer and eligible' column in [our recruits spreadsheet]({{ secrets.data.recruits_url | default("/redacted.html") }}). -- [ ] If the phone call interview was more than three days before the first session, call the participant again to reconfirm the following information: - - [ ] Remind the participant that any jewelry should be removed prior to the scan. - - [ ] Indicate that they MUST shave the upper area of their chest where the ECG electrodes will be placed, if there is hair. The ECG electrodes MUST directly contact the skin. - - [ ] Confirm clothing: - - [ ] if allowed to wear street clothes, remind the participant to avoid clothing with metal or that would uncomfortable to lie in for the duration of the scan; otherwise - - [ ] remark the participant they will be given a gown and they will need to change before every session. - - [ ] Repeat at what time and where will you meet the participant. - - [ ] Verify that the participant has your phone number {{ secrets.phones.study | default("███") }} to call you in case he gets lost. - - [ ] **FEMALE PARTICIPANTS ONLY**: Remind the participant that pregnant women cannot undergo our MRI protocols. Therefore, they will take a pregnancy test (which we will have prepared) before the first session. -- [ ] If participant has indicated nervousness or history of claustrophobia, organize a session to use the mock scanner. - -## BEFORE DAY OF SCAN - -- [ ] Print [the informed consent form](../assets/files/icf_FR.pdf) (**first session only**), an MRI safety screener ([EN](../assets/files/safety_form_EN.pdf)|[FR](../assets/files/safety_form_FR.pdf)) and a receipt form for each participant that will get scanned. -- [ ] Make sure you have internet access, and update the [HCPh-fMRI-tasks repository](https://github.com/TheAxonLab/HCPh-fMRI-tasks) on *{{ secrets.hosts.psychopy | default("███") }}*: - ``` - git fetch upstream - git checkout main - git rebase upstream/main - ``` -- [ ] On the *{{ secrets.hosts.psychopy | default("███") }}* laptop, open a terminal and execute `conda deactivate`. -- [ ] Open psychopy 3 by typing `psychopy` -- [ ] Load in the different experiments and check for proper functioning: - - [ ] {{ settings.psychopy.tasks.func_rest }} (resting-state fMRI): - - [ ] time it to [confirm the length](#task-timing), and - - [ ] check that the movie is played. - - [ ] {{ settings.psychopy.tasks.func_bht }} (breath-holding task, BHT): - - [ ] time it to [confirm the length](#task-timing), and - - [ ] check that the movie is played. - - [ ] {{ settings.psychopy.tasks.func_pct }} (positive-control task, PCT): - - [ ] time it to [confirm the length](#task-timing), and - - [ ] check that the movie is played. +??? important "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 GA to the BIOPAC as described above. +- [ ] Connect the BIOPAC to the *Physiology recording laptop* ({{ secrets.hosts.acqknowledge | default("███") }}) as described above. +- [ ] Connect the *AcqKnowledge* License Key into a USB Port of the *Physiology recording laptop* ({{ secrets.hosts.acqknowledge | default("███") }}). +- [ ] Open *AcqKnowledge* software on the *Physiology recording laptop* ({{ secrets.hosts.acqknowledge | default("███") }}). +- [ ] Open the template *graph file* ([`EXP_BASE.gtl`](../assets/files/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`. diff --git a/docs/data-collection/scanning.md b/docs/data-collection/scanning.md index b9e30792..bf3c7552 100644 --- a/docs/data-collection/scanning.md +++ b/docs/data-collection/scanning.md @@ -42,21 +42,22 @@ ## Acquire a localizer (*AAhead_scout*) - [ ] Indicate the participant that the scanning will soon start: - > Hey [NAME], we are about to start our first scan run. - > - > This is going to be a long session, so please make sure you are feeling as comfortable as you possibly can in there. - > Remember not to cross your legs or hold your hands together and check your back is also comfortable. - > I'm going to ask you to take a deep breath now, so I can check the respiration belt is properly set up. - > If it is too tight, please let me know. - > - > [Allow a few moments for the participant to breathe while you check the recordings] - > - > Okay, we seem to be able to track your respiration. Is the respiration belt too restraining? - > This is also a good moment to swallow, and to check your neck and head are in a comfortable position. - > - > For this first part, all you have to do is stay still; you can relax and close your eyes if it helps. - > - > Are you ready? + ???+ quote "Tell the participant that we are starting" + Hey [NAME], we are about to start our first scan run. + + This is going to be a long session, so please make sure you are feeling as comfortable as you possibly can in there. + Remember not to cross your legs or hold your hands together and check your back is also comfortable. + I'm going to ask you to take a deep breath now, so I can check the respiration belt is properly set up. + If it is too tight, please let me know. + + [Allow a few moments for the participant to breathe while you check the recordings] + + Okay, we seem to be able to track your respiration. Is the respiration belt too restraining? + This is also a good moment to swallow, and to check your neck and head are in a comfortable position. + + For this first part, all you have to do is stay still; you can relax and close your eyes if it helps. + + Are you ready? - [ ] Wait for the participant confirmation and set the speaker off afterward. - [ ] Launch the `AAhead_scout_{32,64}ch-head-coil` protocol by pressing *Continue* (**⯈**). @@ -86,7 +87,7 @@ - [ ] Open the `dwi-dwi_dir-{RL,LR,PA,AP}__279dir_monopolar` sequence and under the section *Diff.*, uncheck all the derivatives except for *Diff. Weighted Image*. ## Acquire the diffusion MRI run - + - [ ] [Adjust the FoV](scanning-notes.md#setting-the-fov) of the `dwi-dwi_dir-{RL,LR,PA,AP}__279dir_monopolar` sequence as indicated below. - [ ] Verify again the `dwi-dwi_dir-{RL,LR,PA,AP}__279dir_monopolar` parameters under section *Diff.* All the derivatives MUST be unchecked except for *Diff. Weighted Image*. - [ ] Inform the participant that the diffusion scan will follow. @@ -102,15 +103,15 @@ ???+ quote "Participant of Cohort II" Hey [NAME], the next block is a bit long, around 30 minutes. - + You can close your eyes and even sleep if you wish. - + I'm going to give you a short time (ten seconds or so) to swallow, and perhaps accommodate your back or your arms. However, please try not to move your head. - + It is critical that you don't move, especially at all at the very beginning and the next 20 seconds after you hear the first blipping sounds. - + Try to minimize swallowing, and eye movements (for example, blinking) and try to maintain comfortable and shallow breathing. - + Are you ready? - [ ] Launch the diffusion `dwi-dwi_dir-{RL,LR,PA,AP}__279dir_monopolar` sequence by pressing *Continue* (**⯈**). @@ -124,7 +125,7 @@ - [ ] Launch the DWI-EPI sequence `fmap-epi_acq-b0_dir-{RL,LR,PA,AP}__6dir_monopolar` for *B0* field mapping by pressing *Continue* (**⯈**). - [ ] While it is running, [adjust the FoV](scanning-notes.md#setting-the-fov) for the following sequence. - [ ] Launch the GRE (*phase difference*) sequence `fmap-phasediff__gre` for *B0* field mapping by pressing *Continue* (**⯈**). -- [ ] While it is running, +- [ ] While it is running, - [ ] [Adjust the FoV](scanning-notes.md#setting-the-fov) for the following sequence. - [ ] Verify that in the next sequence parameters under *Contrast>Reconstruction* the option *Magnitude et phase* is selected! - [ ] Launch the BOLD-EPI sequence `fmap-epi_acq-bold_dir-{RL,LR,PA,AP}__cmrr_me4_sms4` for *B0* field mapping by pressing *Continue* (**⯈**). @@ -136,18 +137,19 @@ ## Acquire the functional MRI block - [ ] Inform the participant about the fMRI block - > Hey [NAME], we are now to move into measuring the activity of your brain. - > - > Is everything alright thus far? - > - > [Allow some time for response] - > - > Before we start, we need to calibrate the eye-tracker device, which follows your right eye during experiments. - > - > Your are going to see a round fixation point, and the point is going to move randomly over the screen space. - > Please follow it with your gaze, trying to look at it as stable as possible and without moving your head. - > - > Are you ready? + ???+ quote "Starting the fMRI block - calibrating the eye tracker" + Hey [NAME], we are now to move into measuring the activity of your brain. + + Is everything alright thus far? + + [Allow some time for response] + + Before we start, we need to calibrate the eye-tracker device, which follows your right eye during experiments. + + Your are going to see a round fixation point, and the point is going to move randomly over the screen space. + Please follow it with your gaze, trying to look at it as stable as possible and without moving your head. + + Are you ready? - [ ] Wait for confirmation, respond to follow-up comments, and [initiate the ET calibration (instructions below)](scanning-notes.md#eye-tracker-calibration) @@ -155,17 +157,18 @@ - [ ] Verify that the task's program is awaiting the scanner's trigger to start. - [ ] Inform the participant that we will proceed with the positive control task (PCT). Repeat task instructions. - > Hey [NAME], thanks for your collaboration with the eye tracking calibration. - > - > The following block will collect some behavioral data and requires your collaboration. - > You will be exposed to several activities. - > - > Whenever you see a red circle, please fix your gaze on it, wherever it is shown on the screen. - > If the red circle moves, we ask you to follow it with your eyes. - > - > Some other times, you'll see either "RIGHT" or "LEFT" written on the screen. During those times, please tap your thumb and the other fingers of your right or left hand as indicated on the screen. - > - > Before we start, please leave the alarm button on your tummy to free your hand for finger tapping. Please do not hesitate to grab it in case you need to squeeze it. + ???+ quote "Starting the positive control task" + Hey [NAME], thanks for your collaboration with the eye tracking calibration. + + The following block will collect some behavioral data and requires your collaboration. + You will be exposed to several activities. + + Whenever you see a red circle, please fix your gaze on it, wherever it is shown on the screen. + If the red circle moves, we ask you to follow it with your eyes. + + Some other times, you'll see either "RIGHT" or "LEFT" written on the screen. During those times, please tap your thumb and the other fingers of your right or left hand as indicated on the screen. + + Before we start, please leave the alarm button on your tummy to free your hand for finger tapping. Please do not hesitate to grab it in case you need to squeeze it. - [ ] Launch the `func-bold_task-pct_dir-{RL,LR,PA,AP}__cmrr_me4_sms4` protocol by pressing *Continue* (**⯈**). - [ ] Wait for the calibration scans to be finished (the process is reported on the bottom left corner of the console) and verify that the first volume's trigger signal was received by *{{ secrets.hosts.psychopy | default("███") }}* (meaning **CHECK that the task program was initiated**). @@ -179,22 +182,24 @@ ### Resting state fMRI - [ ] Inform the participant: - > Thanks [NAME], that was a short behavioral task. - > - > Before moving on, we will run another calibration of the eye tracker, please follow the moving fixation point. - > - > Is everything alright? + ???+ quote "Quick re-calibration the ET before continuing" + Thanks [NAME], that was a short behavioral task. + + Before moving on, we will run another calibration of the eye tracker, please follow the moving fixation point. + + Is everything alright? - [ ] Wait for confirmation, respond to follow-up comments, and [initiate the ET calibration (instructions below)](scanning-notes.md#eye-tracker-calibration) - [ ] Once the ET is calibrated, verify that the task is left and awaiting for the sequence's trigger to start. - [ ] Inform the participant that the next sequence is resting-state fMRI (rsfMRI). - > Hey [NAME], we are about to start resting-state fMRI. - > - > For this scan, all you have to do is stay still, and look at the movie. - > Please do not close your eyes, and it is particularly critical that you don't move at all in the initial moments of the acquisition block. - > - > Are you ready? + ???+ quote "Starting the resting-state block" + Hey [NAME], we are about to start resting-state fMRI. + + For this scan, all you have to do is stay still, and look at the movie. + Please do not close your eyes, and it is particularly critical that you don't move at all in the initial moments of the acquisition block. + + Are you ready? - [ ] Launch the rsfMRI sequence `func-bold_task-rest_dir-{RL,LR,PA,AP}__cmrr_me4_sms4` by pressing *Continue* (**⯈**). - [ ] While it is running: @@ -206,37 +211,40 @@ ### Breath-holding task (BHT) - [ ] Inform the participant: - > Thanks [NAME], that was a long behavioral block. - > - > Before moving on, we will run another calibration of the eye tracker, please follow the moving fixation point. - > - > Is everything alright? + ??? quote "Quick re-calibration the ET before continuing" + Thanks [NAME], that was a long behavioral block. + + Before moving on, we will run another calibration of the eye tracker, please follow the moving fixation point. + + Is everything alright? - [ ] Wait for confirmation, respond to follow-up comments, and [initiate the ET calibration (instructions below)](scanning-notes.md#eye-tracker-calibration) - [ ] Once the ET is calibrated, verify that the task is left and awaiting for the sequence's trigger to start. - [ ] Inform the participant that the next sequence is breath-holding task fMRI. Repeat the instructions for the task. - > Hey [NAME], we will proceed now with a breath-holding task. - > - > I remind you that you have to breathe following the cues of the colored rectangle. - > - > Green means "BREATHE IN", orange means "BREATHE OUT" and red means "HOLD YOUR BREATH". - > - > Remember to not follow the breathing instructions during the first block and to exhale the small amount of air you have remaining at the end of the hold. - > - > Are you ready? + ???+ quote "Starting the breath-holding task" + Hey [NAME], we will proceed now with a breath-holding task. + + I remind you that you have to breathe following the cues of the colored rectangle. + + Green means "BREATHE IN", orange means "BREATHE OUT" and red means "HOLD YOUR BREATH". + + Remember to not follow the breathing instructions during the first block and to exhale the small amount of air you have remaining at the end of the hold. + + Are you ready? - [ ] Launch the `func-bold_task-bht_dir-{RL,LR,PA,AP}__cmrr_me4_sms4` sequence by pressing *Continue* (**⯈**). -- [ ] While it is running, determine whether there is enough time to run the anatomical T2-weighted run. If so, [adjust the FoV](scanning-notes.md#setting-the-fov) for the following sequence. +- [ ] While it is running, determine whether there is enough time to run the anatomical T2-weighted run. If so, [adjust the FoV](scanning-notes.md#setting-the-fov) for the following sequence. - [ ] Once the sequence is over, you need to stop manually the psychopy task by pressing the key t on the keyboard (as fast as possible to avoid collecting more data than needed). ## Concluding the session !!! warning "ONLY if time permits" - + - [ ] Launch the `anat-T2w__flair` protocol by pressing *Continue* (**⯈**) - [ ] Inform the participant: - > Thanks [NAME], the session has concluded and we will shortly let you out of the scanner. + ???+ quote "Session is finished" + Thanks [NAME], the session has concluded and we will shortly let you out of the scanner. - [ ] The exam is over, you can proceed with the [tear-down protocol](./tear-down.md). diff --git a/docs/data-collection/tear-down.md b/docs/data-collection/tear-down.md index d33a7d4d..c0db9ebd 100644 --- a/docs/data-collection/tear-down.md +++ b/docs/data-collection/tear-down.md @@ -13,9 +13,10 @@ - [ ] Help the participant sit down. - [ ] Instruct the participant to remove the earplugs and dispose of them. Ask them about the experience: - > [NAME], how was your experience? - > Have you been able to feel comfortable throughout the session? - > What advice, indication do you feel we could've provided you for a better experience? + ???+ quote "Get feedback about the session from the participant" + [NAME], how was your experience? + Have you been able to feel comfortable throughout the session? + What advice, indication do you feel we could've provided you for a better experience? - [ ] Lift the nasal cannula and help the participant remove it from their head. - [ ] Disconnect the tube from the RB and then lift the velcro attachmet to remove the RB. @@ -41,7 +42,7 @@ - [ ] Take the projector's screen off and store it in its designated shelf. - [ ] Unplug the two cables connected to the ET (signal and power). Put those extremities aside far from the scanner. - [ ] Take the ET back outside and put it in a stable place. - - [ ] Unscrew the ET lens, while **ALWAYS** keeping one hand under the lens while screwing/unscrewing it and put it back into its cover. + - [ ] Unscrew the ET lens, while **ALWAYS** keeping one hand under the lens while screwing/unscrewing it and put it back into its cover. ![cover-mri-compatible-lens](../assets/images/cover-mri-compatible-lens.png "Cover MRI compatible lens") @@ -68,7 +69,7 @@ - [ ] Put the bed back in place = push the "home" button on the scanner - [ ] Put the wooden stopper of the main access tube back on the tube. - [ ] Everything that is removed for the experiment MUST be put back in place at the end of the experiment, i.e. position of the bed, coil, emergency button, ears padding. - - [ ] Take a glove, on the right there is some cleaning napkins. Use them to clean the bed. + - [ ] Take a glove, on the right there is some cleaning napkins. Use them to clean the bed. - [ ] Exit and close the external door. ## AFTER SCAN, outside scanner room @@ -79,12 +80,12 @@ - [ ] Insert a USB key into *{{ secrets.hosts.psychopy | default("███") }}* and save the experiment from AcqKnowledge. - [ ] Upload to a pre-designated drop-box (e.g., using Dropbox) - [ ] Press Ctrl+Alt+Q on the ET's computer to exit the EyeLink 1000 Plus Host PC application and click on the Shutdown button from the **File Manager** toolbar. -- [ ] Switch off laptop and ET PC Tower. Plug back the sync box and the VGA projector where they were. +- [ ] Switch off laptop and ET PC Tower. Plug back the sync box and the VGA projector where they were. - [ ] Fix the rolled cable with the scotch on the PC Tower base. - [ ] Turn off the pump of the GA, then switch the GA off. **DO NOT PUT THE CAP IN WHILE THE PUMP IS ON.** - [ ] Remove the cables connected to the BIOPAC and the GA and store them in the boxes in their original bags. -- [ ] Take the ET, Remove (always with and hand under the lens) the MRI compatible LENS. Put it back to its contained inside the box. -- [ ] Put back the regular Lens. +- [ ] Take the ET, Remove (always with and hand under the lens) the MRI compatible LENS. Put it back to its contained inside the box. +- [ ] Put back the regular Lens. - [ ] Bring back the box and the base at CIBM EEG lab. Put the keys back under old Nora's desk. - [ ] Fix the ET with the scotch at the chariot. - [ ] Bring back the chariot and the TMS laptop at the TMS lab diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index f78b0767..8b4be4e4 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -54,4 +54,22 @@ span.flip { -o-transform: scale(-1, -1); -ms-transform: scale(-1, -1); transform: scale(-1, -1); +} + +/*:root { + --md-admonition-icon--thanks: fa-thumbs-up; +}*/ +.md-typeset .admonition.thanks, +.md-typeset details.thanks { + border-color: rgb(43, 155, 70); +} +.md-typeset .thanks > .admonition-title, +.md-typeset .thanks > summary { + background-color: rgba(43, 155, 70, 0.1); +} +.md-typeset .thanks > .admonition-title::before, +.md-typeset .thanks > summary::before { + background-color: rgb(43, 155, 70); + -webkit-mask-image: var(--md-admonition-icon--thanks); + mask-image: var(--md-admonition-icon--thanks); } \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 85a1d5a5..ab42d68f 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -30,9 +30,16 @@ theme: primary: black logo: assets/images/chuv_logo.svg features: - - tabs + # - tabs + - navigation.instant + # - navigation.tabs + - navigation.expand + - navigation.top - content.code.copy - content.code.annotate + icon: + admonition: + thanks: fontawesome/solid/thumbs-up plugins: - search From e26ecd356d238ed452c97980595686bb455d3c3b Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Mon, 28 Aug 2023 15:35:12 +0200 Subject: [PATCH 2/2] Apply suggestions from code review Co-authored-by: esavary --- docs/data-collection/participant-prep.md | 2 +- docs/data-collection/preliminary.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/data-collection/participant-prep.md b/docs/data-collection/participant-prep.md index 3dd38e3c..acf44f17 100644 --- a/docs/data-collection/participant-prep.md +++ b/docs/data-collection/participant-prep.md @@ -120,7 +120,7 @@ - [ ] Offer the participant a box to deposit everything they have in their pockets and all jewelry/hair accessories, and indicate the clothing to enter the scanning room: ??? quote "*Dress code* inside the scanner **if they need to CHANGE INTO SCRUBS**" - Before we continute, we need to make sure we do not introduce any dangerous object in the magnet room. + Before we continue, we need to make sure we do not introduce any dangerous object in the magnet room. Here you will find a changing room [SHOW THEM THE CHANGING ROOM]. I have prepared some scrubs for you. diff --git a/docs/data-collection/preliminary.md b/docs/data-collection/preliminary.md index 043df515..be3f408a 100644 --- a/docs/data-collection/preliminary.md +++ b/docs/data-collection/preliminary.md @@ -36,7 +36,7 @@ flowchart TB sb --->|USB| pc1["Stimuli presentation Laptop ({{ secrets.hosts.psychopy | default("███") }})"] pc1 <--->|Ethernet| et pc1 --->|USB| modem[MMBT-S Interface] - pc1 --->|HDMI| display[Proyector] + pc1 --->|HDMI| display[Projector] modem --->|25-pin parallel| biopac4 BIOPAC --->|Ethernet| pc2["Physio-recording Laptop ({{ secrets.hosts.acqknowledge | default("███") }})"]