# annotate\_amplitude for a specific time window

**URL:** <https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329>\
**Category:** Support & Discussions\
**Tags:** preprocessing, eeg\
**Created:** [July 26, 2022, 6:55am UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329 "2022-07-26T06:55:03Z")\
**Posts on this page:** 20\
**Page:** 1

<div class="post-metadata">

**Author:** ![FranziMNE](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/franzimne/32/2366_2.png) [@FranziMNE](https://mne.discourse.group/u/FranziMNE)\
**Post date:** [July 26, 2022, 6:55am UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/1 "2022-07-26T06:55:03Z")

</div>

Hello everyone,

for my EEG data I want to artifact reject based on an amplitude threshold (-100 to +100 µV) and a joint probability threshold (SD = 5), but only for the first second after stimulus onset. My trials are 9 seconds long, and of course I can just epoch the data to the first second and run the annotation on it. But after this procedure I need my 9 sec epochs back. I am not sure how to tell python to integrate the corrected first second to the rest 8 seconds.

Thank you!

Franzi

---

<div class="post-metadata">

**Author:** ![sappelhoff](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sappelhoff/32/3276_2.png) [@sappelhoff](https://mne.discourse.group/u/sappelhoff)\
**Post date:** [July 27, 2022, 7:30am UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/2 "2022-07-27T07:30:13Z")

</div>

You could:

1. epoch your data in the first second
2. run annotate\_amplitude
3. save the epoch indices that are considered bad
4. epoch your data with your 9 seconds
5. apply the indices you have saved before to reject the “bad” epochs

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [July 27, 2022, 8:23am UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/3 "2022-07-27T08:23:03Z")

</div>

> [@sappelhoff](#):
>
> - epoch your data in the first second
> - run annotate\_amplitude

`annotate_amplitude()` only works with continuous (“raw”) data.

---

<div class="post-metadata">

**Author:** ![sappelhoff](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sappelhoff/32/3276_2.png) [@sappelhoff](https://mne.discourse.group/u/sappelhoff)\
**Post date:** [July 27, 2022, 9:53am UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/4 "2022-07-27T09:53:21Z")

</div>

> [@richard](#):
>
> `annotate_amplitude()` only works with continuous (“raw”) data.

right, thanks for the reminder Richard.

I think in that case I’d recommend using `.get_data`, numpy, and custom code.

Something like:

```python
time_of_interest = epochs.time_as_index([0, 1]) # from 0 to 1 seconds
data = epochs.get_data() # (n_epochs, n_channels, n_times)
for epoch in data:
    # epoch is a numpy array (n_channels, n_times)
    epoch_window = epoch[:, time_of_interest[0]:time_of_interest[1]]
    # epoch_window is the first second of your data
    ... # and so on

```

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [July 27, 2022, 10:05am UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/5 "2022-07-27T10:05:16Z")

</div>

> [@sappelhoff](#):
>
> ```python
> epoch_window = epoch[:, time_of_interest[0]:time_of_interest[1]]
> 
> ```

Probably should use `epochs.time_as_index()` here to get the correct time indices!

---

<div class="post-metadata">

**Author:** ![FranziMNE](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/franzimne/32/2366_2.png) [@FranziMNE](https://mne.discourse.group/u/FranziMNE)\
**Post date:** [August 8, 2022, 5:13pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/6 "2022-08-08T17:13:21Z")

</div>

Thank you for your help  
I tried to run the following code

```python
time_of_interest = data.time_as_index([0, 1]) # from 0 to 1 seconds
data1 = data.get_data() # (n_epochs, n_channels, n_times)
for epoch in data1:
    # epoch is a numpy array (n_channels, n_times)
    epoch_window = data1[:, time_of_interest[0]:time_of_interest[1]]
    
reject_criteria = dict(eeg=100e-6)       
flat_criteria = dict(
                     eeg=-100e-6)

data_annot = mne.Epochs(epoch_window, events, tmin=0, tmax=1, reject_tmax=0,
                    reject=reject_criteria, flat=flat_criteria,
                    reject_by_annotation=False, preload=True)
data_annot.plot_drop_log()

```

It says undefined “events”. But when I do define the events it says "‘EpochsFIF’ object has no attribute ‘annotations’

```python
time_of_interest = data.time_as_index([0, 1]) # from 0 to 1 seconds
data1 = data.get_data() # (n_epochs, n_channels, n_times)
for epoch in data1:
    # epoch is a numpy array (n_channels, n_times)
    epoch_window = data1[:, time_of_interest[0]:time_of_interest[1]]
    
all_events, all_event_id = mne.events_from_annotations(data)    
event_id = slice(all_event_id, 'Stimulus/S ')
events, _ = mne.events_from_annotations(data, event_id=event_id)

reject_criteria = dict(eeg=100e-6)       
flat_criteria = dict(
                     eeg=-100e-6)

data_annot = mne.Epochs(epoch_window, events, tmin=0, tmax=1, reject_tmax=0,
                    reject=reject_criteria, flat=flat_criteria,
                    reject_by_annotation=False, preload=True)
data_annot.plot_drop_log()

```

Any idea how to handle this problem?

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [August 8, 2022, 5:21pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/7 "2022-08-08T17:21:04Z")

</div>

> [@FranziMNE](#):
>
> But when I do define the events it says "‘EpochsFIF’ object has no attribute ‘annotations’

If I read your code correctly, you pass `data` to `events_from_annotations()`; however, this function expects a `Raw` and not an `Epochs` object.

Since you already managed to create epochs, there must be events somewhere??! You should just re-use them.

Best,

Richard

---

<div class="post-metadata">

**Author:** ![FranziMNE](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/franzimne/32/2366_2.png) [@FranziMNE](https://mne.discourse.group/u/FranziMNE)\
**Post date:** [August 8, 2022, 5:55pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/8 "2022-08-08T17:55:24Z")

</div>

Yes I defined the events before running the ICA  
I already tried to include the code here:

```python
#define functions
def slice(sourcedict, string):
    newdict = {}
    for key in sourcedict.keys():
        if key.startswith(string):
            newdict[key] = sourcedict[key]
    return newdict

def flux_eegEpochs (raw_load):
    
    reject_criteria = dict(eeg=100e-6)       
  flat_criteria = dict(
                     eeg=-100e-6)

    all_events, all_event_id = mne.events_from_annotations(raw_load)
    print(all_event_id)
    print(all_events[:5])
   
    #Reload events chooseing only the ones that start with 'Stimulus/S '
    event_id = slice(all_event_id, 'Stimulus/S ')
    events, _ = mne.events_from_annotations(raw_load, event_id=event_id)

    # Epoch data
    epochs = mne.Epochs(raw_load, 
                    events, 
                    event_id=event_id, 
                    tmin=-1, 
                    tmax=8,
                    detrend=1,
                    reject=reject_criteria, 
                    flat=flat_criteria,
                    reject_by_annotation=False,
                    #baseline=(-0.2,0),
                    proj=True,
                    preload=True)

    len(epochs.events)
    
    return epochs

    epochs.plot_drop_log()

```

Doesnt work unfortunatly

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [August 8, 2022, 6:29pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/9 "2022-08-08T18:29:03Z")

</div>

Since your event names all start with `Stimulus/`, we can abuse MNE’s event name grouping capability: you can trivially select all `Stimulus` epochs via

```python
epochs_stim = epochs['Stimulus']

```

No need to slice etc.

Does that help solve your problem?

---

<div class="post-metadata">

**Author:** ![FranziMNE](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/franzimne/32/2366_2.png) [@FranziMNE](https://mne.discourse.group/u/FranziMNE)\
**Post date:** [August 9, 2022, 7:16am UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/10 "2022-08-09T07:16:32Z")

</div>

Unfortunatly not. It does help to get rid of the “event” error but then it says "Flat value must be a number \>= 0, not “-0.0001”, if I change it to “0” what I actually dont want because I want a -100 flat and +100 peak, it gives me the following error: “No appropriate channels found for the given picks (array(, dtype=int32))”

```python
 epochs = mne.Epochs(raw_load, 
                    events, 
                    event_id=event_id, 
                    tmin=-1, 
                    tmax=8,
                    detrend=1,
                    reject=reject_criteria, 
                    flat=flat_criteria,
                    reject_by_annotation=False,
                    #baseline=(-0.2,0),
                    proj=True,
                    preload=True)

    len(epochs.events)
    
    return epochs

    epochs.plot_drop_log()

def identify_ica(raw):
    """ Use ICA to reject artifacts
    """
    # Perform ICA
    ica = mne.preprocessing.ICA(
            n_components=20, # Number of components to return
            max_pca_components=None, # Don't reduce dimensionality too much
            random_state=0,
            max_iter=800,
            verbose='INFO')
    ica.fit(raw, reject_by_annotation=True)
    
    # Plot ICA results
    
    ica.plot_components(inst=raw) # Scalp topographies - Click for more info
    ica.plot_sources(raw) # Time-courses - click on the ones to exclude
    
    return ica

raw_load=mne.io.read_raw_fif('C:\\Users\Admin\Desktop\Projekt_Franziska\Studie 3\Analyse\EEG\BIDS_mast\sub-56\ses-Expo\eeg/sub-56_ses-Expo_run01_data_interpolated.fif', verbose=False)
mne_data_folder ='C:\\Users\Admin\Desktop\Projekt_Franziska\Studie 3\Analyse\EEG\BIDS_mast\sub-56\ses-Expo\eeg/'

print(raw_load.annotations)
print(len(raw_load.annotations))
print(set(raw_load.annotations.duration))
print(set(raw_load.annotations.description))
print(raw_load.annotations.onset[0])

dataepoch=flux_eegEpochs (raw_load)
print(dataepoch.info)

filt_data = dataepoch.copy()
filt_data.load_data().filter(l_freq=1., h_freq=None)

raw_ica=identify_ica(filt_data);

```

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [August 9, 2022, 12:40pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/11 "2022-08-09T12:40:17Z")

</div>

Hello @FranziMNE, it’s become difficult for me to figure out which line exactly is causing the error you’re reporting. Could you please try to reduce your code snippet to the relevant lines only, and also share the entire traceback when you post error messages? This should make it easier for others to understand where things are going wrong.

Best wishes,  
Richard

---

<div class="post-metadata">

**Author:** ![FranziMNE](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/franzimne/32/2366_2.png) [@FranziMNE](https://mne.discourse.group/u/FranziMNE)\
**Post date:** [August 9, 2022, 1:07pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/13 "2022-08-09T13:07:33Z")

</div>

Got it, no epochs were left when I set the reject\_criteria to the stringent threshold I used, so no epochs were left in the ICA, resulting in that error.  
So I think everything can be traced back to the reject\_criteria.

For the critera: Why cant I set the flat criteria to -100 microVolt? I actually want to have those criteria: amplitude threshold (-100 to +100 µV) and a joint probability threshold (SD = 5)

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [August 9, 2022, 3:27pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/14 "2022-08-09T15:27:36Z")

</div>

> [@FranziMNE](#):
>
> Why cant I set the flat criteria to -100 microVolt?

The rejection thresholds are specified as so-called “peak-to-peak amplitude”, PTP.

This is basically the signal change from the lowest to the highest point. Therefore, the value can never be negative.

What you’re asking for is, to my knowledge, not supported. But I’m not sure if this is actually a problem — I believe the concept of PTP is actually better suited for artifact rejection, as it’s independent of signal baseline and DC offset.

Best wishes,  
Richard

---

<div class="post-metadata">

**Author:** ![FranziMNE](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/franzimne/32/2366_2.png) [@FranziMNE](https://mne.discourse.group/u/FranziMNE)\
**Post date:** [August 9, 2022, 3:47pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/15 "2022-08-09T15:47:54Z")

</div>

Alright! 🙂 The backround ist just, that for my current paper, reviewers asked to redo our EEG analysis since the preprocessing pipeline differs between ERP and TFR analysis in the paper. This is due the fact that my co-author ran the ERP analysis with matlab and I did the TFR analysis in python. I now set up the ERP analysis in python and try to build up the pipeline my co-author used. He used the mentioned artifaction correction criteria. This is why I wanted to redo them in python.  
Thank you very much for your help again! 🙂

Best, Franzi

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [August 9, 2022, 4:06pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/16 "2022-08-09T16:06:42Z")

</div>

I just don’t think there’s a trivial way to do it… @agramfort may have an idea?

---

<div class="post-metadata">

**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\
**Post date:** [August 10, 2022, 2:35pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/17 "2022-08-10T14:35:43Z")

</div>

> [@FranziMNE](#):
>
> For the critera: Why cant I set the flat criteria to -100 microVolt? I actually want to have those criteria: amplitude threshold (-100 to +100 µV)

I think you mis-understand what `flat` means here. both `reject` and `flat` must be positive, and reflect absolute values of signal amplitudes. If you want to reject epochs that have values _above_ 100 microvolts and also _below_ -100 microvolts, then all you need to specify is `reject=100` (actually, `100e-6`, since MNE-Python stores data in Volts, not microvolts). `flat` is used to reject epochs where the signal stays _below_ a given absolute value for the _entire epoch_ (as an indication that something went wrong with the connection / the active electrode’s amplifier isn’t working / whatever).

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [August 10, 2022, 6:07pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/18 "2022-08-10T18:07:36Z")

</div>

> [@drammock](#):
>
> and reflect absolute values of signal amplitudes. If you want to reject epochs that have values _above_ 100 microvolts and also _below_ -100 microvolts, then all you need to specify is `reject=100` (actually, `100e-6`, since MNE-Python stores data in Volts, not microvolts)

**Objection** 😉

It’s **not** signal amplitudes, it’s the **peak-to-peak** amplitudes! That is, the difference between the highest and the lowest value.

> **[Amplitude | Peak-to-peak amplitude](https://en.wikipedia.org/wiki/Amplitude#Peak-to-peak_amplitude)**
>
> Peak-to-peak amplitude (abbreviated p–p) is the change between peak (highest amplitude value) and trough (lowest amplitude value, which can be negative). With appropriate circuitry, peak-to-peak amplitudes of electric oscillations can be measured by meters or by viewing the waveform on an oscilloscope. Peak-to-peak is a straightforward measurement on an oscilloscope, the peaks of the waveform being easily identified and measured against the graticule. This remains a common way of specifying ampli...

But your suggestion does do the trick for the scenario pointed out here, I believe, yes! So my previous statement:

> [@richard](#):
>
> I just don’t think there’s a trivial way to do it

is actually incorrect.

But I just wanted to clarify the nomenclature here a little.

---

<div class="post-metadata">

**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\
**Post date:** [August 10, 2022, 6:12pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/19 "2022-08-10T18:12:38Z")

</div>

> [@richard](#):
>
> It’s **not** signal amplitudes, it’s the **peak-to-peak** amplitudes!

ah, of course you are right. The main point stands (that `flat` is not appropriate here) but `reject` will not be sufficient by itself. I wonder if we should allow `reject` to take a callable?

---

<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [August 10, 2022, 6:20pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/20 "2022-08-10T18:20:22Z")

</div>

> [@richard](#):
>
> But your suggestion does do the trick for the scenario pointed out here, I believe, yes! So my previous statement:
> 
> > [@richard](#):
> >
> > I just don’t think there’s a trivial way to do it
> 
> is actually incorrect.

Actually … no, this is **not** the case. Say if you specify `reject={'eeg': 100e-6}` and within a given epoch, the minimum signal amplitude is `40 µV` and the maximum is `120 µV`, the absolute amplitude exceeds 100 µV but the PTP does not, so the epoch is retained.

We cannot “fix” this by specifying an additional `flat` parameter either, because this one also only looks at PTP.

> [@drammock](#):
>
> I wonder if we should allow `reject` to take a callable?

I believe this would be the best approach that grants us greatest flexibility without forcing us to introduce a new parameter. @FranziMNE could then just use a function like:

```python
def custom_reject(single_epoch_data):
    if (
        single_epoch_data().min() < -100e-6 or
        single_epoch_data().max() > +100e-6
    ):
        return False # reject
    else:
        return True # keep

```

---

<div class="post-metadata">

**Author:** ![FranziMNE](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/franzimne/32/2366_2.png) [@FranziMNE](https://mne.discourse.group/u/FranziMNE)\
**Post date:** [August 12, 2022, 4:01pm UTC](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329/21 "2022-08-12T16:01:10Z")

</div>

Hi 🙂 Thanks for the idea

```python
# Load data (after ICA)
subject = 'sub-52'
session = 'ses-Expo'
bids_root ='C:\\Users\\Admin\\Desktop\\Projekt_Franziska\Studie 3\\Analyse\\EEG\\BIDS_mast'
mne_data_folder=bids_root + '/' + subject + '/' + session + '/' + 'eeg/' 
data=mne.read_epochs(mne_data_folder + subject + '_' + session + '_run01_' + 'data_ica.fif', verbose=False)

def custom_reject(data):
    if (
        data().min() < -100e-6 or
        data().max() > +100e-6
    ):
        return False # reject
    else:
        return True # keep

data.plot_drop_log()

```

It sadly doesnt reject anything, even when changing the criteria to very unreasonable low values

[Next page](https://mne.discourse.group/t/annotate-amplitude-for-a-specific-time-window/5329.md?page=2)