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htwangtw / adie_ongoingthoughts

ADIE ongoing thought related analysis plan
MIT License
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[FEAT] Convert task fMRI event logs #14

Open htwangtw opened 3 years ago

htwangtw commented 3 years ago

The event logs related to the task fMRI recording is now stored under: /path/to/projects/critchley_adie/BIDS_data/sourcedata/fmri_event_logs We need to convert the logs to BIDS standard event files, the Spike2 file to BIDS physio format, and add the spike2 file to derivatives/physio_smr/ with BIDS format file name and mirror the directory structure of the main BIDS data.

After the fMRI files being converted by @willstrawson using heudiconv, there should be place holder event files. Create new functions in adie/events.py to populate event logs to the BIDS event files (see BIDS specification). Source content for the event logs are wri and/or log can be found in /path/to/projects/critchley_adie/BIDS_data/sourcedata/fmri_event_logs. Relevant smr files can be converted with existing functions created by @htwangtw, with new naming rules.

Alternatively, a script stored under bin/ that does the job would be fine too.

@htwangtw is happy to review your solutions.

willstrawson commented 3 years ago

Will make a start on this

willstrawson commented 3 years ago

I'm just trying to find the best fmri event file. In each fmri_even_logs/[adie/control]/mindwandering/[ADIE/CONADIE]XXX/ there's 5 files: 2 files (.smr, .s2rx) are physiological data; one file (.wri) contains one line like 'Pulse Tranist Time(s): 412.5'; the .mat file contains info regarding participant ID, gender, pulse transit time, and VAS Questions but no VAS ratings; and finally, the .log file which contains time-varying data. So it seems this .log is the only suitable candidate for determining event timings.

However, the only info in these files are Time, and whether the key was pressed UP or DOWN. Nothing regarding what was showing on the screen at each time point. @htwangtw Are you aware of any other files which may provide more information on events? Thanks

htwangtw commented 3 years ago

Nope. You will need to contact people who are involved in data collection to find out.

willstrawson commented 3 years ago

Cool cool i'll start asking around 👍

htwangtw commented 3 years ago

If you have a look at adie/spike.py that's the function you can use to covert spike file to BIDS.