adding annotations to raw array

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1

I am looking at ecog data that has x channels. There is no stimulus channel. The data has events 1 – thumb movement, 2 – index finger movement. I have added these events as annotations (which are all numpy array) like below to the raw array.

`annotations = mne.Annotations(onset, duration, stim_id.astype(str)) ) #stim_id is the id of event

raw.set_annotations(annotations)`

When I print the annotations, I get :
print(annotations)
<Annotations | 60 segments: 1 (30), 2 (30)>
but when I print raw.annotations it is an empty array
print(raw.annotations)
<Annotations | 0 segments>

Wondering why the annotations are not getting added to the raw array?

2

And obviously when I tried to get events from annotations , it was an empty list as well

events_from_annot, event_dict = mne.events_from_annotations(raw)

print(events_from_annot)

[ ]

3

It’s probably an issue with the first_samp/origin of time/measurement date. Basically, your annotation are likely “outside” of your recording. I think when you do raw.set_annotations you get a message close to “omitting 60 annotations outside of range”.

In the Notes of Annotations, you have a graph-like code block which details the different (and messy) interaction of those 3 parameters. Copy/pasting below:

----------- meas_date=XX, orig_time=YY -----------------------------

     |              +------------------+
     |______________|     RAW          |
     |              |                  |
     |              +------------------+
 meas_date      first_samp
     .
     .         |         +------+
     .         |_________| ANOT |
     .         |         |      |
     .         |         +------+
     .     orig_time   onset[0]
     .
     |                   +------+
     |___________________|      |
     |                   |      |
     |                   +------+
 orig_time            onset[0]'

----------- meas_date=XX, orig_time=None ---------------------------

     |              +------------------+
     |______________|     RAW          |
     |              |                  |
     |              +------------------+
     .              N         +------+
     .              o_________| ANOT |
     .              n         |      |
     .              e         +------+
     .
     |                        +------+
     |________________________|      |
     |                        |      |
     |                        +------+
 orig_time                 onset[0]'

----------- meas_date=None, orig_time=YY ---------------------------

     N              +------------------+
     o______________|     RAW          |
     n              |                  |
     e              +------------------+
               |         +------+
               |_________| ANOT |
               |         |      |
               |         +------+

            [[[ CRASH ]]]

----------- meas_date=None, orig_time=None -------------------------

     N              +------------------+
     o______________|     RAW          |
     n              |                  |
     e              +------------------+
     .              N         +------+
     .              o_________| ANOT |
     .              n         |      |
     .              e         +------+
     .
     N                        +------+
     o________________________|      |
     n                        |      |
     e                        +------+
 orig_time                 onset[0]'

Have a look at raw.info["meas_date"] which should be None or a datetime and have a look at raw.first_samp. Then you will need to modify your onsets accordingly.

Mathieu

4

Just to second that, you should just have to add raw.first_samp to your variable onset