fix: correct typos in documentation across multiple files

Author: jaimebarran

docs/debi/data-processing/1_1_et_QAQC_of_mreye_data.md

@@ -951,7 +951,7 @@ filtered_coor_data_LIBRE, Preserve_mask, Discard_mask = filter_XY_coord(coor_dat
      398.6000061]
     Y_coord [         nan          nan          nan ... 302.1000061  301.79998779
      300.1000061 ]
-    After cleaning nan, eminating data affected by blinking,            and preserving the fixation 
+    After cleaning nan, eliminating data affected by blinking,            and preserving the fixation 
     The length of X coordinate data: 374558
     The length of Y coordinate data: 374558
 
@@ -999,7 +999,7 @@ filtered_coor_data_LIBRE, Preserve_mask, Discard_mask = filter_XY_coord(coor_dat
      398.6000061]
     Y_coord [         nan          nan          nan ... 302.1000061  301.79998779
      300.1000061 ]
-    After cleaning nan, eminating data affected by blinking,            and preserving the fixation 
+    After cleaning nan, eliminating data affected by blinking,            and preserving the fixation 
     The length of X coordinate data: 374558
     The length of Y coordinate data: 374558
 
@@ -1042,7 +1042,7 @@ filtered_coor_data_LIBRE, Preserve_mask, Discard_mask = filter_XY_coord(coor_dat
      398.6000061]
     Y_coord [         nan          nan          nan ... 302.1000061  301.79998779
      300.1000061 ]
-    After cleaning nan, eminating data affected by blinking,            and preserving the fixation 
+    After cleaning nan, eliminating data affected by blinking,            and preserving the fixation 
     The length of X coordinate data: 374558
     The length of Y coordinate data: 374558
 
@@ -1320,7 +1320,7 @@ def cal_event_stat(event_duration):
 
     return event_stat_dict
 
-def voilinplot(subject_event_dict, event,color='skyblue'):
+def violinplot(subject_event_dict, event,color='skyblue'):
     sub_num = len(subject_event_dict)
     event_duration_list=[]
     for idx in range(sub_num):
@@ -1403,9 +1403,9 @@ A violin plot combines the features of a box plot and a density plot, making it
 
 
 ```python
-voilinplot(subject_event_dict, event='blink', color='skyblue')
-voilinplot(subject_event_dict, event='saccade',color='coral')
-voilinplot(subject_event_dict, event='fixation',color='teal')
+violinplot(subject_event_dict, event='blink', color='skyblue')
+violinplot(subject_event_dict, event='saccade',color='coral')
+violinplot(subject_event_dict, event='fixation',color='teal')
 ```
 
 

docs/debi/data-processing/2_MRI_post_processing.md

@@ -118,7 +118,7 @@ The scripts about how to use mitosius please refer to the [Monalisa document](ht
 
 ### Recon function
 
-In our reconstruction, we utilize `Steva` function for Single-frame Least-square Regularized Reconstruction, where reularizaiton is the l1-norm of spatial gradient of the image.
+In our reconstruction, we utilize `Steva` function for Single-frame Least-square Regularized Reconstruction, where regularization is the l1-norm of spatial gradient of the image.
 The reconstructed results are in the format of `**.mat`.
 You can find more details in the [Monalisa document](https://mattechlab.github.io/monalisa/2-2_reconstruction_calls.html#steva).
 

docs/flexyphy/data-collection/data-collection_flexyphy_protocol.md

@@ -9,7 +9,7 @@ The acquisition of N=10 subjects was be collected in compliance with the ethical
 
 ## Overall experimental setting
 
-The goal of this setting is to compare several trajectories (3 trajectories: the standard phyllotaxis, uniform phillotaxis, and flexiphy) on two different acquisition sequences associated to two different visual tasks: a GRE sequence with central fixation task and a LIBRE sequence with a moving dot task.
+The goal of this setting is to compare several trajectories (3 trajectories: the standard phyllotaxis, uniform phyllotaxis, and flexiphy) on two different acquisition sequences associated to two different visual tasks: a GRE sequence with central fixation task and a LIBRE sequence with a moving dot task.
 
 The goal is to obtain anatomical T1w MRI scan with synchronized eye tracking recording (the right eye gaze trajectories and eye movement events including blinking, saccades and fixation).
 
@@ -91,7 +91,7 @@ Ensure the projector beam is directed into the scanner room.
 - Plug the other end of the cable into the SyncBox.
 ![rj45-2](../../assets/debi_protocol/selected/6-e2-rj45-plugged.png){: style="width: 80%;display: block; margin: 0 auto;"}
 - Turn on the SyncBox
-- Check syncrohonization
+- Check synchronization
     - [ ] Enter the <span class="syncbox">Synchronization</span> mode by selecting it and pushing the enter button :fontawesome-solid-circle:{ .bluecolor }.
     - [ ] Hit the down arrow button :fontawesome-solid-caret-down:{ .bluecolor } until you find <span class="syncbox">Send triggerpulse to PC</span>
     - [ ] Push the enter button :fontawesome-solid-circle:{ .bluecolor } every time you want to send an <span class="keypress">s</span> character.
@@ -186,7 +186,7 @@ Ensure the projector beam is directed into the scanner room.
 
 !!! danger "Go through the Information to the participant section."
 - Sign the ICF and go through the experimental instructions one more time.
-- Make sure any metallic object (necklace, earring, piercing, elements in the pockts, e.g coins, etc) is correctly removed before entering the scanner room. Sometimes, boots and bras have metallic parts too. 
+- Make sure any metallic object (necklace, earring, piercing, elements in the pockets, e.g coins, etc) is correctly removed before entering the scanner room. Sometimes, boots and bras have metallic parts too. 
 
 ##### Place the subject on the bed
 

docs/general/emergency-procedures.md

@@ -74,7 +74,7 @@
 
 At any moment, you may determine that the participant will require medical attention:
 
-  - The participant's health has been threatened or is actively at risk (e.g., elevated heart frequency, lack of pulse, respiratory issues, unconsciousness, dizzyness, unsteadyness, etc.)
+  - The participant's health has been threatened or is actively at risk (e.g., elevated heart frequency, lack of pulse, respiratory issues, unconsciousness, dizziness, unsteadiness, etc.)
   - The participant is unresponsive
   - The participant reports feeling unwell and needs attention
   - You think they may need medical attention but you are unsure.

docs/general/et-related/et_software_install.md

@@ -2,7 +2,7 @@
 
 ## 1 EyeLink Installation
 
-- The EyeLink MUST be installed before PyEDFRead and Pychopy.
+- The EyeLink MUST be installed before PyEDFRead and PsychoPy.
 - Register a new account for downloading the EyeLink Developers Kits. [Link for installation](https://www.sr-research.com/support/forumdisplay.php?fid=3).
 - The activation of the new account might take up for 24 hours.
 - Install the EyeLink Developer Kit and EyeLink Data Viewer following the instructions.

docs/general/notes-scanning.md

@@ -53,7 +53,7 @@
     - [ ] Drag and drop the protocol's stack icon (🗇) corresponding to the `anat-T1w__mprage` sequence into the image viewer.
         The icon will appear AFTER the image has been acquired.
 
-- [ ] Make sure that the FOV (yellow square) includes the whole brain by tilting or translating the FOV. If the full brain, including the cerebellum, do not fit in the FOV, favorise making sure that the cortex is fully enclosed in the yellow square. For reproducibility, it is better if the FOV across sequences have a similar center and a similar tilt. However, if it is not possible, the priority remains to include the whole brain in the FOV.
+- [ ] Make sure that the FOV (yellow square) includes the whole brain by tilting or translating the FOV. If the full brain, including the cerebellum, do not fit in the FOV, prioritize making sure that the cortex is fully enclosed in the yellow square. For reproducibility, it is better if the FOV across sequences have a similar center and a similar tilt. However, if it is not possible, the priority remains to include the whole brain in the FOV.
 - [ ] If two sequences have the same resolution and the same number of slices, you can copy paste the FOV
     - [ ] Open the sequence for which you want to adjust the FOV/geometry
     - [ ] Right click on the sequence for which the FOV has already been carefully positioned
@@ -112,7 +112,7 @@
     - [ ] Once finished, click on the floppy disk icon (:fontawesome-solid-floppy-disk:) in the upper left to save.
     - [ ] Give the protocol a relevant name starting with the date of acquisition in the format YYYYMMDD and click <span class="consolebutton">Save</span>.
         ![](../assets/general/notes-scanning/save_protocol6.jpg)
-    - [ ] If desired, the protocol details can also be downloaded as a pdf on a peripherical USB key.
+    - [ ] If desired, the protocol details can also be downloaded as a pdf on a peripheral 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).
@@ -135,7 +135,7 @@
 - [ ] Turn off the satellite station ({{ secrets.hosts.console_left | default("███") }}, the computer on the left side of the control desk)
 - [ ] Turn off the control station ({{ secrets.hosts.console_right | default("███") }}, the computer on the right side of the control desk)
 - [ ] Wait for both computers to shut down.
-- [ ] Push the blue button displaying an overdotted circle and the **SYSTEM OFF** label above, which is found right above the key
+- [ ] Push the blue button displaying an over-dotted circle and the **SYSTEM OFF** label above, which is found right above the key
 - [ ] Turn the key into the *closed lock* position (:fontawesome-solid-lock:)
 
 ---
@@ -208,7 +208,7 @@ There are two options to extract the participant, when the session has concluded
 
 | ![take_table_down](../assets/general/notes-scanning/take_table_down.png) | ![quick_return](../assets/general/notes-scanning/quick_return.png) |
 |:--:|:--:|
-| *The participant can be extracted by pressing the extraction button (bottom arrow in the leftmost picture) and then genly rolling the central knob. Alternatively, you can just press the* Home :fontawesome-solid-house: *button (rightmost picture).* {: colspan=2} |
+| *The participant can be extracted by pressing the extraction button (bottom arrow in the leftmost picture) and then gently rolling the central knob. Alternatively, you can just press the* Home :fontawesome-solid-house: *button (rightmost picture).* {: colspan=2} |
 
 
 ---