wmvanvliet

import numpy as np
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis, _class_cov, _class_means, \
    linalg
from sklearn.base import BaseEstimator
from scipy.spatial.distance import euclidean, correlation


class Euclidean2(BaseEstimator):

    _estimator_type = 'distance'

wmvanvliet

import matplotlib.pyplot as plt
import mne
import numpy as np
from scipy import sparse

# We will operate on the fsaverage source space. Fetch it first.
subjects_dir = mne.datasets.sample.data_path() / "subjects"
mne.datasets.fetch_fsaverage(subjects_dir)

# Load the source space.

wmvanvliet

"""Virtually move around head position."""

import os
from copy import deepcopy
from subprocess import run

import mne
import numpy as np

from move_head import move_head

wmvanvliet

import neurodsp
import neurodsp.aperiodic
import neurodsp.plts
import neurodsp.sim
import neurodsp.spectral
import numpy as np
from pyrasa.irasa import irasa

n_seconds = 10
fs = 500  # sampling rate in Hz

wmvanvliet

import pickle


class MyClass:
    """Example class to pickle. Version 2."""

    def __init__(self, a, b, c, d=4):
        """New field `d` with default value, so no problems right?"""
        self.a = a
        self.b = b

wmvanvliet

"""Interface between python and the MEG hardware at Aalto's MEG core.

This is intended to be used in combination with PsychoPy to perform classic experiments
involving simple events and responses.

Example that presents a visual stimulus, sends a trigger code to the MEG and waits for a
button response with one of the response pads:

>>> from psychopy import core, visual
>>> from aalto_meg import AaltoMEG

wmvanvliet

#!/bin/bash

# Start tmux
tmux new -d -s "slurm$SLURM_JOB_ID"

# Make job wait for user to connect
sleep 8h

wmvanvliet

"""Plot a cluster.

Plot the spatial extend of a cluster (as those returned from the cluster-based
permutation stats) on a brain.

Author: Marijn van Vliet <w.m.vanvliet@gmail.com>
"""

import mne
import numpy as np

wmvanvliet

"""
Plot the spatial extent of a cluster (as those returned from the cluster-based
permutation stats) on a brain.

Author: Marijn van Vliet <w.m.vanvliet@gmail.com>
"""

import mne
import numpy as np

wmvanvliet

"""
Obtain head -> MRI transform for the MOUS dataset for use with MNE-Python.

If you want to analyze the "Mother of all unification studies" dataset with
FreeSurfer and MNE-Python, you will need the MRI->HEAD coordinate
transformations. In the original dataset, the T1w_space_CTF.nii files contain
this information, but it takes some doing to distill this into a transform
object as used by MNE-Python.

This script assumes you have ran FreeSurfer on the T1w.nii files of all the