I need to output the EEG data after annotations. However, the output files I get are only with annotations and not containing EEG + annotations data. With save containing EEG + annotations data ?
Raw objects have a
raw.save() method that saves the data and annotations. Annotations can be saved in a separate file via
raw.annotations.save(). To reconstruct later, there is
mne.read_annotations() followed by
Is there some reason that this won’t work for you, and you must store the annotations in the same file as the data?
The annotations on data I can output. However the data containing both the EEG Sign + Annotations I can’t get.
I need to cut out the EEG data in the interval of the crisis, and mark points of interest with Annotations.
And output that data to use another moment.
Do you have an example? It is better to understand!
I cannot reproduce the problem. Here is an example where I add an annotation, save the raw file, and when I reload the raw file the annotation is there.
import os import mne # load sample data sample_data_folder = mne.datasets.sample.data_path() sample_data_raw_file = os.path.join(sample_data_folder, 'MEG', 'sample', 'sample_audvis_raw.fif') raw = mne.io.read_raw_fif(sample_data_raw_file) raw.crop(0, 10).load_data() # annotate ann = mne.Annotations(onset=4, duration=3, description='TestingTesting') raw.set_annotations(ann) # save-load roundtrip filename = 'foo-raw.fif' raw.save(filename, overwrite=True) del raw loaded_raw = mne.io.read_raw(filename) print(loaded_raw.annotations)
That’s how it should work.
raw.save saves everything contained in the
raw object, which includes annotations.
But there is no way to cut the data, save it in a new .EEG file?containing only data winth annotations!
I’m not certain that I understand what you want to do. Raw objects have a
.crop() method for “cutting” the data. Are you trying to remove the part that has the annotation, or to keep the annotated part and remove the rest of the data?
Other things that might be helpful:
.save()method saves in the
.fifformat, not in the
.EEGformat (which is BrainVision I think?). We don’t currently support export to BrainVision, but MNE-BIDS can write BrainVision format I think.
if you are trying to exclude the annotated part, you can make your annotation start with the letters
BADand then various MNE-Python functions can automatically ignore it (using a
reject_by_annotation=Trueparameter). That way there is no need to actually remove the bad data segment from the file; you can leave it in and it will be ignored.
Small correction: pybv can export to BrainVision.