Step 2: Acquire data¶
Once everything is set up correctly, data can be collected as usual. However, issues can always arise during data acquisition. If data collection is interrupted or specific data cannot be collected as expected, it is important to address this on site.
Problem Handling¶
Document any problem that occurs and how it was handled. Make sure to also keep track of any unusual event during data acquisition. This information should go into the known issues with the data or missing data section of the README.md and might also be relevant for the sessions.tsv.
Below is a summary of typical interruptions and recommended actions:
| Interruption Type | Recommended Action Summary |
|---|---|
| Interrupted sequence | Delete incomplete run, export only the correct run |
| Subject position changed | Repeat scout (and fmap if needed), delete incomplete run |
| Sequence not repeated | Export the incomplete/interrupted sequence |
| Interrupted session | See details below for within-same-meeting or new meeting |
Two typical problems that may come up during data acquisition and should be handled immediately to prevent issues during conversion are:
Interrupted sequence¶
There are many reasons why a sequence on the MR might have been interrupted and repeated.
Here we need to distinguish between three different cases:
1. Sequence restarted¶
The sequence was stopped and restarted, whereby the second run represents the data you want.
Recommended steps:
- Delete the interrupted sequence
- Export only the run of the sequence you want
For later data processing, it will seem like the interruption never happened. Still, if the sequence was already running for a while and thus the subject might have an additional training effect in any task, this should be documented.
2. Subject position changed¶
The sequence was stopped, the subject position changed, and then the sequence was restarted.
Recommended steps:
- Run the scout and, if needed, the fmap again
- Delete the interrupted sequence
- Export only the run of the sequence you want
- Export the additional fmap
3. Sequence wasn't repeated¶
The sequence was stopped, but not repeated. The incomplete data of the interrupted sequence should be used. (This is a fairly rare case.)
Recommended steps:
- Export the interrupted sequence
Interrupted session¶
Sessions may be interrupted for various reasons and can be resumed either within the same meeting or in a subsequent meeting.
1. Resumption within the same meeting¶
A typical example for this use case is if the subject needs to go to the toilet in between.
Recommended steps:
- Do not end the scanning session while the subject has left
- When the subject is back in position, repeat the scout and, if needed, mapping sequences
- Continue with the next incomplete sequence
- Export the session as usual: all complete sequences, no interrupted sequences, and fieldmaps (two sets in case they were reacquired)
2. Resumption at a new meeting¶
The session terminates. The subject leaves and returns for a follow-up meeting on another day.
Recommended steps:
- Export all completed sequences of the first part of the session
- Do not merge the data into your data repository before the session is completed
- When the session continues, start it with the same acquisition name