Brezovec conversion

[h-mayorquin]

This is to organize the conversion. Some general resources.

Fictrac:
https://github.com/rjdmoore/fictrac/tree/master

The paper:
https://www.biorxiv.org/content/10.1101/2022.03.20.485047v1

I will update as more information comes

[h-mayorquin]

To-do:

• Add conversion notes. Brezovec conversion I #1
• Add support for fictrac ingestion. Use FicTracDataInterface from neuroconv instead of ad-hoc interface. #4
• Add videos Add video to interface #6
• Build a NIfTI format imaging extractor based on bruker. Add imaging extractor #3
• Add an imagine interface (or two) that adds both the anatomical and functional data to the nwbfile. Add imaging interfaces #10
• Figure out alignment between Fictract and the functional imaging. According to the paper, the anatomical observations were done "immediately after" the functional imaging. Account for this. Add session start times #8
• Set start times for FicTrac neuroconv PR
• Check timing for the VideoInterface. Add camera device #17
• Check metadata: General and Subject Add subject, general and imaging metadata #12
• Check metadata: Imaging Add subject, general and imaging metadata #12
• Check metadata: Video [add camera device] Add camera device #17
• Check metadata: FicTrac [add units scaled by ratio] Add radius to FicTrac conversion #16
• Add new alignment schema, Add temporal alignment #22
• Fix the path expansion to work on the whole data Add subjects from json mapping #24
• Add preprocessing add nifti interface for processed data #25
• Be sure that the subjects are propertly mapped as per the file that the autors shared with us Add subjects from json mapping #24
• Run a stub conversion for the data we have an use the inspector.
• Run the full conversion for testing.
• Run the inspector.
• ulpload the data
• Test that the conversion can be run with the requirements.

[h-mayorquin]

Code to extract the datetime of fictract @alessandratrapani:

from pathlib import Path
from datetime import datetime
from zoneinfo import ZoneInfo

folder_path = Path("/home/heberto/Clandinin-CN-data-share/brezovec_example_data/fictrac")
file_path = folder_path / "fictrac-20200620_122048.dat"
assert file_path.is_file(), f"File path {file_path} does not exist."

def read_first_timestamp_from_file(file_path):
    with open(file_path, 'r') as file:
        # Read the first data line
        first_line = file.readline()
        
        # Split by comma and extract the timestamp (the 22nd column)
        timestamp = float(first_line.split(',')[21]) / 1000.0  # Transform to seconds
        
    return timestamp

def convert_to_los_angeles_time(utc_timestamp):
    # Convert the timestamp to a UTC datetime object
    utc_time = datetime.utcfromtimestamp(utc_timestamp).replace(tzinfo=ZoneInfo("UTC"))

    # Convert the UTC time to Los Angeles local time
    los_angeles_tz = ZoneInfo('America/Los_Angeles')
    los_angeles_time = utc_time.astimezone(los_angeles_tz)

    return los_angeles_time

timestamp = read_first_timestamp_from_file(file_path)
la_time = convert_to_los_angeles_time(timestamp)
print(la_time)

We should have similar functions to extract the session_start_time from the xml in bruker.

Once we have all the starting times we should follow the proceedure here to set those times right:
https://neuroconv.readthedocs.io/en/main/user_guide/temporal_alignment.html#temporal-alignment-within-nwbconverter

[alessandratrapani]

Once we have all the starting times we should follow the proceedure here to set those times right:
https://neuroconv.readthedocs.io/en/main/user_guide/temporal_alignment.html#temporal-alignment-within-nwbconverter

We need additional information before proceeding with this, correct? For instance, the VoltageRecording_00x.csv file, that should contain the TTL signals for synchronization.

[h-mayorquin]

That would be better, but we can improve on what we have right now by using the information that we already have available. Specially critical is to adjust the starting_time of the anatomy so it is after the functional one. That is, the start time of the functional anatomy should be around 30 minutes from the session_start_time.

[h-mayorquin]

Linking here for provenance:
catalystneuro/neuroconv#598