Merge pull request #47 from celprov/enh/improvement_celine2

ENH : complete scanning protocol and miscalleneous

docs/data-collection/participant-prep.md

@@ -22,7 +22,42 @@
 - [ ] Remind the participant to use the bathroom at this moment if they need ({{ secrets.rooms.bathroom | default("███") }}).
 - [ ] Have participant empty their pockets or change into scrubs, and remove all jewelry/hair accessories and check for any missed metallic objects with the scan center's preferred method.
 - [ ] Instruct participant on staying still and encourage them to request breaks if necessary.
-- [ ] Describe the participant how the session will develop, with special attention to tasks. Answer all the questions that may arise.
+- [ ] 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. Answer all the questions that may arise.
+
+    > There will be three tasks during the session.
+    > The first one will be the resting-state; for this scan, all you have to do is stay still and look at the movie.
+    > Please do not close your eyes.
+    >
+    > The second one is going to be breath-holding task; we will ask you to breathe with a specific pattern following the color of the rectangle.
+    > 
+    > You will watch five repeats of the same block.
+    > The first time the experimental block is shown, please keep your habitual breathing pace disregarding the task instructions.
+    > At the end of this mock block, a message will remind you that you must adapt your breathing to the pace indicated by the color-changing rectangle in the center of the screen for the remaining four repetitions of the block.
+    > Please inhale while the green rectangle is on, and exhale while you see the yellow rectangle.
+    > To tell you that the breath-hold is approaching, the green color will be lighter and the yellow will become orange for the last breathe-in and breathe-out.
+    > Then a red rectangle will follow the last breathe-out (orange color), and you will need to hold your breath throughout.
+    > The red rectangle will become pink to signal that you will soon be able to breathe again.
+    > When the colored rectangle disappears, please exhale any remaining air in your lungs (without  unnatural efforts to push the air out) and breathe normally until the next block starts.
+    > At the end of the breath-hold, please exhale the small amount of air you have remaining so we can measure the CO2 level via the gas analyzer.
+    > We will repeat this block of inhale/exhale 5x followed by hold 6 times. The first time, you must look at the rectangle but ignore the breathing instructions and 
+    > just breath normally. A warning message will indicate when you should start following the breathing clues.
+    >
+    > Any questions about the breath-holding task?
+    >
+    > The third task is a control task. This task is composed of different subtasks.
+    > In the first subtask, a grating pattern will display. Just look at the fixation point represented by a red dot.
+    >
+    > In the second subtask, please follow the points with your eyes.
+    > It is critical that you move your eyes without moving your head.
+    >
+    > In the third subtask, the word left and right will flash alternatively.
+    > Please tap your thumb against your four other fingers sequentially.
+    > Do it with your right hand while the word "RIGHT" is displayed, and correspondingly with your left hand after with the word "LEFT". Stop when the words disappear.
+    > During the finger tapping, you MUST leave the alarm button, e.g., on your belly.
+    > In the fourth subtask, a dot appears at the center of the screen.
+    > Look a the dot until the subtask is finished.
+    >
+    > Is everything clear to you? Do you have any questions?
 - [ ] 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.
     - [ ] Tell the participant that they MUST leave the alarm button, e.g., on their belly, during the positive control task. Indicate that you will remind them of this before starting the task.
 - [ ] Indicate the participant where the door to the changing room is, and ask them to change clothes if necessary.

docs/data-collection/pre-session.md

@@ -43,18 +43,28 @@ Instructions of operations to be performed before the participant arrival, **bef
 ## Setting up the BIOPAC system and physiological recording sensors
 
 - [ ] Ensure you have the AcqKnowledge software USB license key.
-    - [ ] Plug the USB key to the computer *{{ secrets.hosts.acqknowledge | default("███") }}*. It needs to stay plugged at all times during the acquisition as shown in the picture below.
-- [ ] Plug the power cord of the BIOPAC and of the GA into suitable power sockets.
-- [ ] Plug in the Ethernet (the plug is on the back side) to one USB input of *{{ secrets.hosts.acqknowledge | default("███") }}*, using the Ethernet-to-USB adaptor [INSERT PICTURE].
+    - [ ] Plug the USB key to the multiport adapter for Mac and plug that adapter to the computer *{{ secrets.hosts.oesteban | default("███") }}* as shown in the picture below. **It needs to stay plugged at all times during the acquisition.** 
+- [ ] Plug in the Ethernet (the plug is on the back side of the BIOPAC) to the multiport adapter connected to the computer *{{ secrets.hosts.oesteban | default("███") }}*.
     ![biopack-back](../assets/images/biopack-back.jpg "BIOPAC back side")
-    ![biopack-computer](../assets/images/CHUV_computer_setup.jpg "Connect Biopac to the computer")
+    ![mac_setup](../assets/images/mac_setup.png) 
+- [ ] Connect one end of the parallel cable on the parallel plug on the back side of the STP100D unit of the BIOPAC [INSERT PICTURE] and the other end to the parallel port of the NEUROSPEC parallel to USB converter [INSERT PICTURE].
+- [ ] Connect that NEUROSPEC adapter to one of the USB port of the laptop *{{ secrets.hosts.psychopy | default("███") }}*.
+- [ ] Plug the power cords of the BIOPAC and the GA into suitable power sockets.
 - [ ] Go inside the scanning room, unscrew the wood cap that covers the hole in front of the MR.
 - [ ] Check that the extension tube for the nasal cannula does not contain any bubbles.
 - [ ] Delicately pass the extension tube that will be connected to the nasal cannula and the extension tube from the respiration-belt (RB) through the front access tube. 
 ![Tube_setup](../assets/images/Tube_setup.jpg "Tube setup")
-- [ ] Connect the distal end of the extension tube to the cannula via a MLA0343 drying tube and/or the desiccant chamber (?) and leave the cannula ready on the bed ready for the participant. If the color of the drying tube changed, it should be replaced. You should keep enough extension tube inside the MR room so that it can lie on the floor. It is important that both the GA and the RB tubes lay on the floor as much as possible to avoid waves shaking the tubes.
+- [ ] Connect the distal end of the extension tube to the cannula via an MLA0343 drying tube and/or the desiccant chamber (?) and leave the cannula ready on the bed ready for the participant.
+    To connect the drying tube to the cannula, you need to insert with force the end into the cannula.
+    If the color of the drying tube changes, it should be replaced.
+
+    !!! warning "Ensure that the length of the tubing inside the MR room is sufficient so that it can lie on the floor."
+
+        When the tubing is hanging, pressure waves may alter the recorded gas concentration.
+
 ![drying-tube](../assets/images/Drying_Tube.jpg "MLA0343 drying tube")
 - [ ] Connect the distal end of the RB tube to the RB and leave it on the bed.
+![RB_connection](../assets/images/RB_connection.jpg "RB_connection")
 - [ ] Go back to the control room and connect the proximal end of the cannula extension tube to a MLA0110 inline filter.
 ![MLA0110-inline-filter](../assets/images/inline_filter.png "MLA0110 inline filter")
 - [ ] Remove the cap of the gas input (Sample In, front panel of the GA) and connect the MLA0110 inline filter to it. The inline filter MUST be replaced after some ten sessions.
@@ -70,6 +80,7 @@ Instructions of operations to be performed before the participant arrival, **bef
     - [ ] Check that the exhaust pipe (back of the GA) is free of obstruction. An obstructed exhaust can damage the device!
 
 ![gaz-analyser-back](../assets/images/gaz-analyser-back.jpg "Gas Analyzer back")
+
 - [ ] Check that the cap on `Sample In` is removed and that the MLA0110 inline filter is connected to it. The **pump switch MUST BE OFF when the cap is on and when switching on the GA**. Turn the GA on using the on/off switch located at the front of the GA. The GA **MUST be ON for 20-30 min** to warm-up before measuring.
 ![gaz-analyser](../assets/images/gaz-analyser.jpg "Gas Analyzer")
 - [ ] Check that the flow control wheel (front of the GA) is set to the maximum.
@@ -128,7 +139,9 @@ Instructions of operations to be performed before the participant arrival, **bef
     ![pctower](../assets/images/pctower.png)
 
 - [ ] This is the sync box of the scanner, allowing a synchronization of the triggers between the scanner sequence and the ET recordings.
+
     ![syncbox](../assets/images/syncbox.png)
+
 - [ ] Connect to the ET to the *{{ secrets.hosts.psychopy | default("███") }}* laptop with the ethernet cable (blue color).
 
 ![connect-ethernet-to-laptop](../assets/images/connect-ethernet-to-laptop.png)
@@ -138,13 +151,18 @@ Instructions of operations to be performed before the participant arrival, **bef
     ![syncbox-usb](../assets/images/syncbox-usb.png)
 
 - [ ] Connect the *{{ secrets.hosts.psychopy | default("███") }}* laptop to the screen switch box (see picture below) with the corresponding HDMI cable. This should project your screen on the screen of CHUV's tower {{ secrets.hosts.acqknowledge | default("███") }}.
-
     ![switchbox_hdmi](../assets/images/switchbox_hdmi.jpg)
-    ![laptop_connections](../assets/images/laptop_connections.png)
+
+    !!! warning "If the monitor does not automatically switch the source of the screen, you can use the button below to switch it." 
+
+        ![switch_screen](../assets/images/screen_switch.jpg)
+
+- Your laptop connections should now look like this.
+
+    ![laptop_setup](../assets/images/laptop_setup.png)
 
 - [ ] Configure the display settings of the laptop to mirror outputs and set a resolution of 800x600 for both screens. **That step and that exact resolution is crucial for the eye-tracker calibration to work.**
-- [ ] Push the button shown below to project your screen on the second screen.
-    ![switch_screen](../assets/images/screen_switch.jpg)
+
 - [ ] Configure the display settings of the laptop to mirror outputs and set a resolution of 800x600 for both screens.
 - [ ] Double check that the IP address corresponding to the ethernet interface of the *{{ secrets.hosts.psychopy | default("███") }}* laptop is correct. You can either run `ifconfig -a` or use the GUI. Make sure the IP/mask is **100.1.1.2/24**, and the protocol is IP version 4. Execute `ping 100.1.1.1` to see if the ET is responding to echoes.
 - [ ] Check that you can send trigger events manually:
@@ -177,9 +195,10 @@ Instructions of operations to be performed before the participant arrival, **bef
     - [ ] Press enter to begin the *camera setup mode*.
     - [ ] The camera setup mode contains a view of one eye, and you can switch that view between two modes: one is the field-of-view of the ET, the second is an automatic zoom on the eye itself (or a random part if the eye is not visible).
     - [ ] To ease the setup of the ET, switch to the full view in the camera setup mode by pressing the left or right arrow. This will allow you to adjust the ET position as the infrared camera is providing feedback inside the scanning room through the projector.
-    - [ ] On the ET computer, verify that the calibration selected is the 6-points one.
+    - [ ] On the ET computer, verify that the calibration selected is the 9-points one.
         - [ ] Click on `Set Options` on the right of the screen.
-        - [ ] On top left under `Calibration type`, choose the image containing 6 points [INSERT PICTURE].
+        - [ ] On top left under `Calibration type`, choose the image containing 9 points.
+            ![9-points_calibration](../assets/images/9-points_calibration.jpg)
 
 
 ## Final checks inside the scanning room

docs/data-collection/preliminary.md

@@ -23,15 +23,22 @@
 
     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:
-    - [ ] Select all the sequences in the sequence list and click right to copy.
     - [ ] Open the Dot-Cockpit
+        ![](../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`.
-    - [ ] Paste the copied sequences in the empty program [INSERT PICTURE].
+    - [ ] 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 in 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)
+    - [ ] Save the protocol by pressing on the floppy disk icon in the upper left. Give the protocol a relevant name starting with the date of acquisition in the format YYYYMMDD.
+        ![](../assets/images/save_protocol6.jpg)
     - [ ] If desired, the protocol details can also be downloaded as a pdf on a peripherical USB key.
         - [ ] Click right on the protocol and select `Print`
         - [ ] Save the PDF in your USB key.
-    - [ ] Repeat the operation after creating the four variants of the protocol, one per PE direction.
+    - [ ] Repeat the operation to create the four variants of the protocol, one per PE direction.
 
 **Install the BIOPAC**
 
@@ -46,6 +53,7 @@
     - [ ] 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 SPT100 (solid state relay driver unit) is used to record triggers. A trigger appears as a vertical red line on your physiological recordings [INCLUDE IMAGE]. Plug the trigger to the TRIG entrance.
 - [ ] Install the BIOPAC recording software AcqKnowledge.
+- [ ] Ensure that the lever of the NEUROSPEC adapter is set on `s`.
 
 #### Every two months - calibrate the GA