mscheltienne / eeg-flow Goto Github PK

View Code? Open in Web Editor NEW

0.0 0.0 2.0 2.01 MB

License: MIT License

Python 78.07% Jupyter Notebook 21.93%

audio eeg flow oddball

eeg-flow's Introduction

📫 How to reach me: [email protected]

eeg-flow's People

Contributors

Watchers

Forkers

arthurnguyen eegkit

eeg-flow's Issues

Check why lock/release of files fails on windows CIs

xfail to investigate:

eeg-flow/eeg_flow/utils/tests/test_concurrency.py

Line 9 in 7009a1a

 @pytest.mark.xfail(sys.platform == "win32", reason="fails on windows, to investigate.") 

added in #9

Add key press events and mouse press events as annotations

ICA on Raw vs Epochs

@ArthurNguyen Quick thoughts about the ICA on Raw vs Epochs; it's probably better to keep fitting on the entire Raw because the epochs are very short and might not yield enough data points to fit good components.

Thus, to keep a standardize approach, the function to "merge" annotations should be modified to mark as bad the selected bad segments + any oddball annotation overlapping partially or fully with this bad segment (effectively changing the boundaries of the bad segment annotation to an oddball annotation onset and to an oddball annotation offset).

eeg-flow/eeg_flow/utils/annotations.py

Lines 42 to 80 in 8a4d2ef

 def merge_bad_annotations(raw: BaseRaw) -> Annotations: 

 """Merge bad_ and other annotations. 

  Parameters 

  ---------- 

  raw : Raw 

  Raw object with annotations. 

  Returns 

  ------- 

  annotations : Annotations 

  Created annotations where the bad annotations have been removed and 

  annotations overlapping with a bad annotation have been prefixed with 

  bad_. 

  """ 

 annotations = raw.annotations.copy() 

 offset_ = None 

 annotation2remove = list() 

 onsets2edit = list() 

 description2edit = list() 

 for k, annotation in enumerate(annotations): 

 if annotation["description"].lower().startswith("bad"): 

 offset_ = annotation["onset"] + annotation["duration"] 

 annotation2remove.append(k) 

 continue 

 if offset_ is None: 

 continue 

 if annotation["onset"] <= offset_: 

 annotation2remove.append(k) 

 onsets2edit.append(annotation["onset"]) 

 description2edit.append(annotation["description"]) 

 for idx in annotation2remove[::-1]: 

 annotations.delete(idx) 

 description2edit = ["bad_" + elt for elt in description2edit] 

 new_annotations = Annotations(onsets2edit, 0.1, description2edit) 

 annotations += new_annotations 

 return annotations

Response locked, mismatch number of responses and actual correct responses,

eeg-flow/eeg_flow/tasks/epochs_evoked.py

Line 229 in 37f3e59

metadata_reponse = pd.DataFrame.from_dict(metadata_reponse)

Hello,
Dans un exemple ou un enregistrement contient des falses alarms (le participant a appuyé alors qu'il n'aurait pas du),

metadata_reponse["event_name"] va contenir strictement les evenements "responses" dont les faut
metadata_reponse["response_time"] ne contient que les bonnes reponses (== Hits)
Donc il y aura par exemple 36 event_name et 35 response_time

Tu arriverais a voir comment filtrer facilement la premiere partie pour retirer ces mauvaises reponses?
Merci

Arthur

https://we.tl/t-Pisv83JNjC

Step 5 does not stop if file not exist

https://github.com/mscheltienne/eeg-flow/blob/806dcc199e809dc65001897621445f5276b36af2/eeg_flow/tasks/ica_decomposition.py#L343C5-L343C30

Hello,
There's an error here in the step 5, inside of eeg_flow.tasks.label_components

If attempting to open a file where the deratives of step 4 does not exist we expect this behavior:

output: "error, this file does not exist"

What we have instead:

The code seems to continue until it is stuck with this error "Channel CPz already specified in inst."

Add game statistics as misc channels

Interpolation for signal on misc channels with irregular sampling rate

Univariate series: linear? spline?

Add mouse wheel up/down as events

Add simple mastoid/car ERP analysis

Annotations stored in raw.fif already?

greetings

https://github.com/mscheltienne/eeg-flow/blame/c13148b7ef9c33d7c3dfe99df0e0f746c01777b4/scripts/tasks/2_annotate_bad_channels_and_segments.ipynb#L89

_oddball_with_bads_annot.fif of step 2 is actually not loaded in step 3. Can you confirm that the _bads annotations are already stored in step2_raw.fif? in which case no eed to save an annot.fif file?

eeg-flow/eeg_flow/tasks/ica_decomposition.py

Line 72 in c13148b

 # The raw saved after interpolation of bridges already contains bad channels and 

mscheltienne / eeg-flow Goto Github PK

eeg-flow's Introduction

eeg-flow's People

Contributors

Watchers

Forkers

eeg-flow's Issues

Check why lock/release of files fails on windows CIs

Add key press events and mouse press events as annotations

ICA on Raw vs Epochs

Response locked, mismatch number of responses and actual correct responses,

Step 5 does not stop if file not exist

Add game statistics as misc channels

Interpolation for signal on misc channels with irregular sampling rate

Add mouse wheel up/down as events

Add simple mastoid/car ERP analysis

Annotations stored in raw.fif already?

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent

	def merge_bad_annotations(raw: BaseRaw) -> Annotations:
	"""Merge bad_ and other annotations.

	Parameters
	----------
	raw : Raw
	Raw object with annotations.

	Returns
	-------
	annotations : Annotations
	Created annotations where the bad annotations have been removed and
	annotations overlapping with a bad annotation have been prefixed with
	bad_.
	"""
	annotations = raw.annotations.copy()
	offset_ = None
	annotation2remove = list()
	onsets2edit = list()
	description2edit = list()
	for k, annotation in enumerate(annotations):
	if annotation["description"].lower().startswith("bad"):
	offset_ = annotation["onset"] + annotation["duration"]
	annotation2remove.append(k)
	continue
	if offset_ is None:
	continue
	if annotation["onset"] <= offset_:
	annotation2remove.append(k)
	onsets2edit.append(annotation["onset"])
	description2edit.append(annotation["description"])

	for idx in annotation2remove[::-1]:
	annotations.delete(idx)

	description2edit = ["bad_" + elt for elt in description2edit]
	new_annotations = Annotations(onsets2edit, 0.1, description2edit)
	annotations += new_annotations
	return annotations