README.md

Collecting/Uploading Physio Data

This manual walks through collecting and uploading physiological data (heart rate and respiration). The data will be saved using a bid(ish) format. Please gain familiarity with bids if you plan on helping with data collection/working with data; it's pretty great.

Naming References

Shortcut if you know what steps to take, but forgot how to name the files

bids naming templates:

• raw acq files
  • sub-<label>_ses-<label>_acq-
• txt file output (after raw data collection)
  • sub-<label>_ses-<label>_task-<label>(_run-<label>)_physio
    • the parens around run mean this key-value pair is optional

<label> is any alphanumberic combination, but in BETTER_Aging, and BIKE_EXTEND, we will have predictable names.

Bike Extend

• sub-<label>
  • Four digit integer above 2000 (e.g. 2001)
• ses-<label>
  • day1pre
  • day1post
  • day2pre
  • day2post
  • postintervention
• task-<label>(_run-<label>)
  • rest (1, 2, 3)
  • breathhold

Better Aging

• sub-<label>
  • Three digit zero-padded number (e.g. 002, 015, 120)
• ses-<label>
  • pre
  • post
• task-<label>(_run-<label>)
  • rest (1, 2)
  • taskswitch
• Examples
  • valid: sub-004_ses-pre_task-rest_run-1
    • the first run of rest
  • invalid: sub-004_ses-pre_task-taskswitch_run-1
    • there are no other runs of taskswitch, so don't add the run key-label pair
  • valid: sub-004_ses-pre_task-taskswitch

Steps!

The step-by-step guide...

Prerequsite

Make sure the wifi is turned off.

Step 1

Open the VossLab folder on the desktop.

Step 2

Select the project (either BETTER_Aging or BIKE_EXTEND).

Step 3

Create the subject folder within the project folder. It should follow the format sub-<label>.

Step 4

Create the session folder within the subject folder. It should follow the format ses-<label>.

Step 5

At the base of the project folder, open Standard.acq.

Step 6

In the menu bar, select MP150, and from the dropdown select "Set Up Data Acquisition...".

Step 7

After you select "Set Up Data Acquisition...", you should see a page like this.

Step 8

Select the Length/Rate tab in the new window.

Step 9

Click on File... (in the selected window not the file in the top menu along the top of the screen) and select the session folder you just made as the place to save the data (the folder should be empty).

Step 10

Rename the file from Standard.acq to sub-<label>_ses-<label>_acq- (where you replace <label> with the appropriate names). Notice the trailing - after acq; this is intentional, the program will append a 4 digit number after the -.

Step 11

Select save and this window will pop up, we want incrementing number selected, which should be default. Select ok to continue.

Step 12

Test if the file is working correctly by clicking start on the open acknowledge file (which will still have the title Standard.acq). Once you hit start the name of the tab should change to what you named the file with the 4 digit acquisition number.

Step 13

Working with the MRI technicians, start the recordings before each relevant MRI begins, and stop the recording shortly after each relevant MRI ends

Step 14

After you've collected the physio data, open all the useful acquisitions (not the test one), from the session folder into the program.

Step 15

For each acquisition tab, select "Save As...".

Step 16

Choose the correct session directory to place the converted physio data.

Step 17

Rename the file using BIDS conventions following this general template: sub-<label>_ses-<label>_task-<label>(_run-<label>)_physio where the run parameter is optional. (e.g. we need for the rest scans, but not the task scans)

Step 18

Change saving the file from .acq to *.txt*.csv.

Step 19

Select save and you will see another box pop up, select UNIX (LF) line endings.

Step 20

Turn on the wifi to upload the data to github.

Step 21

Follow the git directions to upload the data.

Step 22

Turn off the wifi when you are done!