Neuropycon

https://neuropycon.github.io/ephypype/
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Neuropycon is an open-source multi-modal brain data analysis kit which provides Python-based...
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### Install ephypype from source

Source: https://neuropycon.github.io/ephypype/_sources/auto_workshop/index.rst.txt

Clone the ephypype repository from GitHub and install it in development mode. This is useful for developers or when needing the absolute latest changes.

```bash
$ git clone https://github.com/neuropycon/ephypype.git
$ cd ephypype
$ python setup.py develop
```

--------------------------------

### Workflow Execution Output Example

Source: https://neuropycon.github.io/ephypype/auto_workshop/01_meg/plot_02_events_inverse_stc.html

Example output from workflow execution, showing subject IDs, lists of processed files, and generated output file paths.

```text
sub-01
sub-01
['/home/pasca/Science/workshop/PracticalMEEG/ds000117/derivatives/meg_derivatives/preprocessing_dsamp_workflow/preproc_meg_dsamp_pipeline/_session_id_01_subject_id_sub-01/ica/sub-01_ses-meg_task-facerecognition_run-01_proc-sss_meg_filt_dsamp_ica.fif', '/home/pasca/Science/workshop/PracticalMEEG/ds000117/derivatives/meg_derivatives/preprocessing_dsamp_workflow/preproc_meg_dsamp_pipeline/_session_id_02_subject_id_sub-01/ica/sub-01_ses-meg_task-facerecognition_run-02_proc-sss_meg_filt_dsamp_ica.fif']
/home/pasca/Science/workshop/PracticalMEEG/ds000117/derivatives/meg_derivatives/source_dsamp_full_reconstruction_dSPM_aparc/_subject_id_sub-01/concat_event/sub-01_sss_filt_dsamp_ica-raw.fif
/home/pasca/Science/workshop/PracticalMEEG/ds000117/derivatives/meg_derivatives/source_dsamp_full_reconstruction_dSPM_aparc/_subject_id_sub-01/concat_event/sub-01_sss_filt_dsamp_ica-raw.fif
/home/pasca/Science/workshop/PracticalMEEG/ds000117/derivatives/meg_derivatives/source_dsamp_full_reconstruction_dSPM_aparc/_subject_id_sub-01/concat_event/sub-01_sss_filt_dsamp_ica-raw-eve.fif

<networkx.classes.digraph.DiGraph object at 0x7fdefa0b5b40>
```

--------------------------------

### Install ephypype from PyPI

Source: https://neuropycon.github.io/ephypype/_sources/auto_workshop/index.rst.txt

Install the ephypype package using pip. This is the recommended method for installing the latest stable version.

```bash
$ pip install ephypype
```

--------------------------------

### Configure and Run Reference Interface

Source: https://neuropycon.github.io/ephypype/tutorials/wrap_fieldtrip.html

Configures and runs the Reference interface for rereferencing iEEG data. Requires FieldTrip to be installed and its path correctly set. The output file path is printed upon completion.

```python
ft_path = '/usr/local/MATLAB/R2018a/toolbox/MEEG/fieldtrip-20200327/'
refmethod = 'bipolar'
channels_name = '{"RAM*", "RHH*", "RTH*", "ROC*", "LAM*","LHH*", "LTH*"}'

reference_if = Reference()
reference_if.inputs.data_file = op.join(data_path, 'SubjectUCI29_data.mat')
reference_if.inputs.channels = channels_name
reference_if.inputs.ft_path = ft_path
reference_if.inputs.refmethod = refmethod
reference_if.inputs.script = ''

out = reference_if.run()

print('Rereferenced data saved at {}'.format(out.outputs.data_output))
```

--------------------------------

### Create Ephypype Workflow with FieldTrip Reference Node

Source: https://neuropycon.github.io/ephypype/_sources/tutorials/wrap_fieldtrip.rst.txt

This example shows how to create an Ephypype workflow, encapsulating the FieldTrip Reference interface within a node and connecting it to a data source. This enables the use of the reference node's output as input for subsequent nodes.

```python
import os.path as op
import nipype.pipeline.engine as pe

import ephypype
from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.nodes.FT_tools import Reference
from ephypype.datasets import fetch_ieeg_dataset


base_path = op.join(op.dirname(ephypype.__file__), '..', 'examples')
data_path = fetch_ieeg_dataset(base_path)

ft_path = '/usr/local/MATLAB/R2018a/toolbox/MEEG/fieldtrip-20200327/'
updatesens = 'no'
refmethod = 'avg'
channels_name = '{"LPG*", "LTG*"}'

workflow_name = 'workflow'
main_workflow = pe.Workflow(name=workflow_name)
main_workflow.base_dir = data_path

subject_ids = ['SubjectUCI29']
infosource = create_iterator(['subject_id'], [subject_ids])

template_path = '%s*.mat'
template_args = [['subject_id']]
datasource = create_datagrabber(data_path, template_path, template_args, infields=['subject_id'])

main_workflow.connect(infosource, 'subject_id', datasource, 'subject_id')

reference_node = pe.Node(interface=Reference(), name='Reference')
reference_node.inputs.channels = channels_name
reference_node.inputs.ft_path = ft_path
reference_node.inputs.updatesens = updatesens
reference_node.inputs.refmethod = refmethod
reference_node.inputs.script = ''

main_workflow.connect(datasource, 'raw_file', reference_node, 'data_file')

main_workflow.write_graph(graph2use='colored')  # colored
main_workflow.config['execution'] = {'remove_unnecessary_outputs': 'false'}

# Run workflow locally on 1 CPU
main_workflow.run(plugin='MultiProc', plugin_args={'n_procs': 1})
```

--------------------------------

### Workflow Graph File Path

Source: https://neuropycon.github.io/ephypype/auto_workshop/01_meg/plot_02_events_inverse_stc.html

Example output showing the file path where the workflow graph is saved.

```text
'/home/pasca/Science/workshop/PracticalMEEG/ds000117/derivatives/meg_derivatives/source_dsamp_full_reconstruction_dSPM_aparc/graph.png'
```

--------------------------------

### Install ephypype using pip

Source: https://neuropycon.github.io/ephypype/_sources/index.rst.txt

Installs the ephypype package and jupyter using pip. Ensure MNE python is installed first.

```bash
$ pip install ephypype
$ pip install jupyter
```

--------------------------------

### Load and Print Time-Frequency Parameters

Source: https://neuropycon.github.io/ephypype/_downloads/9db9cdd4bbb411e68f83d88399605850/run_fieldtrip_wf.ipynb

Loads time-frequency analysis parameters from a JSON file and prints them. This step requires the 'params.json' file to be present and correctly formatted. Note that the FieldTrip package must be installed and its path set up for this example to run.

```python
import json  # noqa
import pprint  # noqa
params = json.load(open("params.json"))
pprint.pprint({'time frequency parameters': params["tfr"]})
ft_path = params["tfr"]['fieldtrip_path']
refmethod = params["tfr"]['refmethod']
channels_name = params["tfr"]['channels_name']
```

--------------------------------

### Install packages using conda and pip

Source: https://neuropycon.github.io/ephypype/_sources/auto_workshop/index.rst.txt

Use this command to create a new conda environment with Python 3.10, install packages from a requirements file, and then install jupyter.

```bash
$ conda create -n practicalmeeg python=3.10
$ pip install -r requirements.txt
$ pip install jupyter
```

--------------------------------

### Import necessary libraries

Source: https://neuropycon.github.io/ephypype/_sources/auto_examples/run_fieldtrip_wf.rst.txt

Imports essential libraries for nipype, data handling, and FieldTrip integration. Ensure FieldTrip is installed and its path is correctly set.

```python
# Authors: Annalisa Pascarella <a.pascarella@iac.cnr.it>
# License: BSD (3-clause)

# sphinx_gallery_thumbnail_number = 2

import os.path as op
import numpy as np
import nipype.pipeline.engine as pe

import ephypype
from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.nodes import ImportFieldTripEpochs, Reference
from ephypype.interfaces import TFRmorlet
from ephypype.datasets import fetch_ieeg_dataset
```

--------------------------------

### Initialize and Configure Main Workflow

Source: https://neuropycon.github.io/ephypype/_sources/tutorials/howto.rst.txt

Create a main Workflow instance using pe.Workflow and specify the base directory for storing outputs. This sets up the environment for connecting nodes.

```python
power_analysis_name = 'power_workflow'

main_workflow = pe.Workflow(name=power_analysis_name)
main_workflow.base_dir = data_path
```

--------------------------------

### Fetch iEEG Dataset

Source: https://neuropycon.github.io/ephypype/tutorials/wrap_fieldtrip.html

Fetches the iEEG dataset and sets up the base path for ephypype examples. Ensure ephypype is installed.

```python
import os.path as op
import ephypype
from ephypype.nodes.FT_tools import Reference
from ephypype.datasets import fetch_ieeg_dataset

base_path = op.join(op.dirname(ephypype.__file__), '..', 'examples')
data_path = fetch_ieeg_dataset(base_path)
```

--------------------------------

### Sample Folder Layout

Source: https://neuropycon.github.io/ephypype/tutorial.html

Illustrates a typical MEEG dataset organization with subject subfolders and recording files.

```bash
NeuroPyConData
├── K0015
│   ├── ecg_eog_info.pickle
│   ├── ec_ipynb_report.html
│   ├── eo_ipynb_report.html
│   ├── K0015_rest_raw_tsss_mc_trans_ec.fif
│   └── K0015_rest_raw_tsss_mc_trans_eo.fif
├── K0025
│   ├── ecg_eog_info.pickle
│   ├── ec_ipynb_report.html
│   ├── eo_ipynb_report.html
│   ├── K0025_rest_raw_tsss_mc_trans_ec.fif
│   └── K0025_rest_raw_tsss_mc_trans_eo.fif
├── K0034
│   ├── ecg_eog_info.pickle
│   ├── ec_ipynb_report.html
│   ├── eo_ipynb_report.html
│   ├── K0034_rest_raw_tsss_mc_trans_ec.fif
│   └── K0034_rest_raw_tsss_mc_trans_eo.fif
├── R0008
│   ├── ecg_eog_info.pickle
│   ├── ec_ipynb_report.html
│   ├── eo_ipynb_report.html
│   ├── R0008_rest_raw_tsss_mc_trans_ec.fif
│   └── R0008_rest_raw_tsss_mc_trans_eo.fif
└── R0023
    ├── ecg_eog_info.pickle
    ├── ec_ipynb_report.html
    ├── eo_ipynb_report.html
    ├── R0023_rest_raw_tsss_mc_trans_ec.fif
    └── R0023_rest_raw_tsss_mc_trans_eo.fif

5 directories, 25 files

```

--------------------------------

### Create Main Workflow and Connect Nodes

Source: https://neuropycon.github.io/ephypype/auto_workshop/01_meg/01-run-smri_reconall.html

Sets up the main nipype workflow and connects the output of the reconall_workflow to the input of the bem_generation node.

```python
freesurfer_workflow_name = 'FS_workflow'
main_workflow = pe.Workflow(name=freesurfer_workflow_name)
main_workflow.base_dir = subjects_dir


main_workflow.connect(reconall_workflow, 'recon_all.subject_id',
                      bem_generation, 'sbj_id')

```

--------------------------------

### Initializing the main workflow and setting base directory

Source: https://neuropycon.github.io/ephypype/auto_examples/plot_preprocessing.html

Creates a nipype workflow engine and specifies the base directory for storing output files. This workflow will orchestrate the preprocessing steps.

```python
# workflow directory within the `base_dir`
preproc_pipeline_name = 'preprocessing_workflow'

main_workflow = pe.Workflow(name=preproc_pipeline_name)
main_workflow.base_dir = data_path

```

--------------------------------

### Create Preprocessing Pipeline

Source: https://neuropycon.github.io/ephypype/_sources/auto_examples/plot_preprocessing.rst.txt

Instantiate the preprocessing pipeline by importing and configuring the `create_pipeline_preproc_meeg` function with relevant parameters.

```python
from ephypype.pipelines import create_pipeline_preproc_meeg  # noqa
preproc_workflow = create_pipeline_preproc_meeg(
    data_path, l_freq=l_freq, h_freq=h_freq, down_sfreq=down_sfreq,
    variance=variance, ECG_ch_name=ECG_ch_name, EoG_ch_name=EoG_ch_name,
    data_type=data_type)

```

--------------------------------

### Run and Visualize Workflow

Source: https://neuropycon.github.io/ephypype/_sources/tutorials/howto.rst.txt

This snippet demonstrates how to generate a colored graph of the workflow and then execute it using the MultiProc plugin with 2 processes. It also shows how to configure the workflow to prevent the removal of unnecessary outputs.

```python
# run pipeline:

main_workflow.write_graph(graph2use='colored')  # colored
main_workflow.config['execution'] = {'remove_unnecessary_outputs': 'false'}
main_workflow.run(plugin='MultiProc', plugin_args={'n_procs': 2})
```

--------------------------------

### Run Workflow in Parallel

Source: https://neuropycon.github.io/ephypype/tutorial.html

Starts a workflow to run in parallel on 4 cores. Use this to configure parallel execution.

```bash
$ neuropycon -p MultiProc -n 4 <...>

```

--------------------------------

### Import necessary libraries

Source: https://neuropycon.github.io/ephypype/auto_examples/plot_power.html

Imports essential libraries for data manipulation, workflow creation, and fetching datasets. Ensure these are installed before running.

```python
# Authors: Annalisa Pascarella <a.pascarella@iac.cnr.it>
#          Mainak Jas <mainakjas@gmail.com>
# License: BSD (3-clause)

# sphinx_gallery_thumbnail_number = 2

import os.path as op
import numpy as np
import nipype.pipeline.engine as pe

import ephypype
from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.datasets import fetch_omega_dataset

```

--------------------------------

### Basic Pipeline Input

Source: https://neuropycon.github.io/ephypype/_sources/tutorial.rst.txt

A simple pipeline that takes 'sample1.fif' and 'sample2.fif' as input files. This demonstrates the basic 'input' command usage.

```bash
$ neuropycon input sample1.fif sample2.fif
```

--------------------------------

### Import necessary libraries

Source: https://neuropycon.github.io/ephypype/_sources/auto_examples/plot_power.rst.txt

Imports essential libraries for data manipulation, pipeline creation, and dataset fetching. Ensure these are installed before running.

```python
# Authors: Annalisa Pascarella <a.pascarella@iac.cnr.it>
#          Mainak Jas <mainakjas@gmail.com>
# License: BSD (3-clause)

# sphinx_gallery_thumbnail_number = 2

import os.path as op
import numpy as np
import nipype.pipeline.engine as pe

import ephypype
from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.datasets import fetch_omega_dataset
```

--------------------------------

### Configure and Run Main Workflow

Source: https://neuropycon.github.io/ephypype/_sources/auto_workshop/01_meg/plot_04-preprocessing_inverse.rst.txt

Configures the main workflow to prevent removal of unnecessary outputs and then executes the workflow using the LegacyMultiProc plugin.

```python
main_workflow.config['execution'] = {'remove_unnecessary_outputs': 'false'}
    main_workflow.run(plugin='LegacyMultiProc', plugin_args={'n_procs': NJOBS})
```

--------------------------------

### Import Core Modules

Source: https://neuropycon.github.io/ephypype/_downloads/d5151967f641f12ab39aa60c21fe976a/plot_eeg_preprocessing.ipynb

Imports necessary libraries from nipype and ephypype for pipeline creation and data handling. Ensure these libraries are installed.

```python
import json
import pprint  # noqa
import os
import os.path as op
import nipype.pipeline.engine as pe

from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.pipelines.preproc_meeg import create_pipeline_preproc_meeg
from ephypype.datasets import fetch_erpcore_dataset
```

--------------------------------

### Fetch iEEG dataset and load parameters

Source: https://neuropycon.github.io/ephypype/_downloads/3648391fced145e21629be4ddffb42cb/run_fieldtrip_IF.ipynb

Fetches a sample iEEG dataset and loads configuration parameters from a 'params.json' file. This step prepares the data and settings required for the rereferencing process.

```python
base_path = op.join(op.dirname(ephypype.__file__), '..', 'examples')
data_path = fetch_ieeg_dataset(base_path)

import json  # noqa
import pprint  # noqa
params = json.load(open("params.json"))
pprint.pprint({'time frequency parameters': params["tfr"]})
ft_path = params["tfr"]['fieldtrip_path']
refmethod = params["tfr"]['refmethod']
channels_name = params["tfr"]['channels_name']
```

--------------------------------

### Create Inverse Solution Workflow

Source: https://neuropycon.github.io/ephypype/_sources/auto_examples/plot_inverse.rst.txt

Instantiates the inverse solution pipeline by importing the create_pipeline_source_reconstruction function and passing necessary parameters. This sets up the nodes for Lead Field computation, noise covariance, and inverse solution estimation.

```python
from ephypype.pipelines import create_pipeline_source_reconstruction  # noqa
inv_sol_workflow = create_pipeline_source_reconstruction(
    data_path, subjects_dir, spacing=spacing, inv_method=inv_method, parc=parc,
    noise_cov_fname=noise_cov_fname)

```

--------------------------------

### Create a Pipeline Node

Source: https://neuropycon.github.io/ephypype/_sources/tutorials/howto.rst.txt

Instantiate a pipeline node by calling its creation function, passing necessary parameters and data paths. For example, create_pipeline_power is used here.

```python
power_workflow = create_pipeline_power(data_path, freq_bands, fmin=fmin, fmax=fmax, method=power_method, is_epoched=is_epoched)
```

--------------------------------

### Configure and run the Reference interface

Source: https://neuropycon.github.io/ephypype/_downloads/3648391fced145e21629be4ddffb42cb/run_fieldtrip_IF.ipynb

Initializes and configures the Ephypype Reference interface to apply a bipolar montage. It sets the input data file, channels, FieldTrip path, and rereferencing method, then executes the interface.

```python
# Now we call the interface Reference to apply a bipolar montage to sEEG data
reference_if = Reference()
reference_if.inputs.data_file = op.join(data_path, 'SubjectUCI29_data.mat')
reference_if.inputs.channels = channels_name
reference_if.inputs.ft_path = ft_path
reference_if.inputs.refmethod = refmethod
reference_if.inputs.script = ''

out = reference_if.run()

print('Rereferenced data saved at {}'.format(out.outputs.data_output))
```

--------------------------------

### Run Workflow in Parallel

Source: https://neuropycon.github.io/ephypype/_sources/tutorial.rst.txt

Starts a workflow to run in parallel on 4 cores. Use the '-p' option for parallel processing and '-n' for the number of CPUs.

```bash
$ neuropycon -p MultiProc -n 4 <...>
```

--------------------------------

### Configure and connect Reference node

Source: https://neuropycon.github.io/ephypype/auto_examples/run_fieldtrip_wf.html

Initializes a Reference node for rereferencing sEEG data using bipolar montage. It sets input parameters like channel names, FieldTrip path, and reference method, then connects it to the datasource node.

```python
reference_node = pe.Node(interface=Reference(), name='rereference')
reference_node.inputs.channels = channels_name
reference_node.inputs.ft_path = ft_path
reference_node.inputs.refmethod = refmethod
reference_node.inputs.script = ''

# Then we connect the output of datasource node to the input of reference_node
main_workflow.connect(datasource, 'raw_file', reference_node, 'data_file')

```

--------------------------------

### Import necessary modules

Source: https://neuropycon.github.io/ephypype/_sources/auto_workshop/01_meg/plot_02_events_inverse_stc.rst.txt

Imports required nipype modules and custom ephypype functions for data processing and pipeline creation. Ensure these modules are installed in your environment.

```python
import os.path as op
import json
import pprint  # noqa

import nipype.pipeline.engine as pe
from nipype.interfaces.utility import Function

from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.pipelines.fif_to_inv_sol import create_pipeline_source_reconstruction  # noqa
```

--------------------------------

### Create Test Files

Source: https://neuropycon.github.io/ephypype/_sources/tutorial.rst.txt

Creates two empty files named 'sample1.fif' and 'sample2.fif' in the current directory for testing purposes.

```bash
$ touch sample1.fif sample2.fif
```

--------------------------------

### Create Power Pipeline

Source: https://neuropycon.github.io/ephypype/_downloads/28c69b982ff953f562e5d4eae4bc3c68/plot_power.ipynb

Instantiate the power pipeline node by importing and configuring `create_pipeline_power` with necessary parameters.

```python
from ephypype.pipelines import create_pipeline_power  # noqa
power_workflow = create_pipeline_power(data_path, freq_bands,
                                       fmin=fmin, fmax=fmax,
                                       method=power_method,
                                       is_epoched=is_epoched)
```

--------------------------------

### Import Core Modules for Ephypype Workflow

Source: https://neuropycon.github.io/ephypype/_downloads/50feaf72899c2174bc94bb258fca3e70/plot_ERP.ipynb

Imports necessary libraries from nipype and ephypype for building and executing EEG processing pipelines. Ensure these packages are installed.

```python
import os
import os.path as op

import json
import pprint  # noqa
import ephypype

import nipype.pipeline.engine as pe
from nipype.interfaces.utility import Function

from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.pipelines.preproc_meeg import create_pipeline_evoked
from ephypype.datasets import fetch_erpcore_dataset
```

--------------------------------

### Get Frequency Band Node

Source: https://neuropycon.github.io/ephypype/_modules/ephypype/nodes/utils.html

Creates a Nipype node to extract specific frequency bands of interest. This node relies on an internal auxiliary function `_get_freq_band`.

```python
from ..aux_tools import _get_freq_band

def get_frequency_band(freq_band_names, freq_bands):
    """Create node to get frequency band of interest.

    Parameters
    ----------
    freq_band_names : list of str
        The frequency band names
    freq_bands : list of list
        The interval of frequency bands

    Returns
    -------
    frequency_node : instance of pe.Node
        The node which recover the frequency band of interest.
    """

    frequency_node = pe.Node(interface=Function(
        input_names=['freq_band_name',
                     'freq_band_names',
                     'freq_bands'],
        output_names=['freq_bands'],
        function=_get_freq_band),
        name='get_frequency_node')

    frequency_node.inputs.freq_band_names = freq_band_names
    frequency_node.inputs.freq_bands = freq_bands

    return frequency_node

```

--------------------------------

### Initialize workflow and set base directory

Source: https://neuropycon.github.io/ephypype/auto_examples/run_fieldtrip_wf.html

Creates a nipype workflow named 'time_frequency_analysis' and sets its base directory to the fetched data path. This directory will store the workflow's outputs.

```python
workflow_name = 'time_frequency_analysis'

main_workflow = pe.Workflow(name=workflow_name)
main_workflow.base_dir = data_path

```

--------------------------------

### Get and Plot TFR Results

Source: https://neuropycon.github.io/ephypype/_downloads/9db9cdd4bbb411e68f83d88399605850/run_fieldtrip_wf.ipynb

Retrieves computed TFR files from the workflow directory and plots the power spectrum for each using MNE. Ensure MNE and ephypype.gather are imported.

```python
import mne  # noqa
from ephypype.gather import get_results  # noqa

tfr_files, _ = get_results(main_workflow.base_dir,
                           main_workflow.name, pipeline='tfr_morlet')

for tfr_file in tfr_files:
    power = mne.time_frequency.read_tfrs(tfr_file)
    power[0].plot([0], baseline=(-.3, -.1), mode='logratio',
                  title=power[0].ch_names[1])
```

--------------------------------

### Configuring the data grabber node

Source: https://neuropycon.github.io/ephypype/auto_examples/plot_preprocessing.html

Sets up a data grabber node to locate and retrieve raw MEG data files. The template path and arguments are configured to match the expected file structure.

```python
template_path = '*%s/%s/meg/%s*rest*0_60*raw.fif'
template_args = [['subject_id', 'session_id', 'subject_id']]
datasource = create_datagrabber(data_path, template_path, template_args)

```

--------------------------------

### Main Path Configuration

Source: https://neuropycon.github.io/ephypype/auto_workshop/01_meg/plot_01_meg_preprocessing.html

This snippet shows the main path configuration for the preprocessing pipeline.

```text
*** main_path -> /home/pasca/Science/workshop/PracticalMEEG/ds000117/derivatives/meg_derivatives ***

```

--------------------------------

### Load and Plot Time-Frequency Results

Source: https://neuropycon.github.io/ephypype/auto_examples/run_fieldtrip_wf.html

Loads time-frequency results from workflow files and plots the power spectral density for visualization. Ensure MNE and ephypype are installed and the workflow has been run.

```python
import mne  # noqa
from ephypype.gather import get_results  # noqa

tfr_files, _ = get_results(main_workflow.base_dir,
                           main_workflow.name, pipeline='tfr_morlet')

for tfr_file in tfr_files:
    power = mne.time_frequency.read_tfrs(tfr_file)
    power[0].plot([0], baseline=(-.3, -.1), mode='logratio',
                  title=power[0].ch_names[1])

```

--------------------------------

### Import Necessary Libraries for Ephypype Workflow

Source: https://neuropycon.github.io/ephypype/_downloads/9db9cdd4bbb411e68f83d88399605850/run_fieldtrip_wf.ipynb

Imports essential libraries and modules from nipype, ephypype, and standard Python libraries for building and executing the workflow. Ensure these libraries are installed and accessible.

```python
import os.path as op
import numpy as np
import nipype.pipeline.engine as pe

import ephypype
from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.nodes import ImportFieldTripEpochs, Reference
from ephypype.interfaces import TFRmorlet
from ephypype.datasets import fetch_ieeg_dataset
```

--------------------------------

### Import necessary libraries and load parameters

Source: https://neuropycon.github.io/ephypype/_downloads/2c191d56a51323e1a46bf19ec940822c/plot_04-preprocessing_inverse.ipynb

Imports essential libraries for Nipype, I/O operations, and NeuroPycon pipelines. It also loads experiment parameters from a 'params.json' file and prints them. Ensure 'params.json' is correctly formatted and accessible.

```python
# Authors: Annalisa Pascarella <a.pascarella@iac.cnr.it>
# License: BSD (3-clause)

# sphinx_gallery_thumbnail_number = 1


import json
import pprint  # noqa

import os.path as op
import nipype.pipeline.engine as pe
from nipype.interfaces.utility import IdentityInterface, Function
import nipype.interfaces.io as nio

from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.pipelines.preproc_meeg import create_pipeline_preproc_meeg  # noqa
from ephypype.pipelines.fif_to_inv_sol import create_pipeline_source_reconstruction  # noqa


# Read experiment params as json
params = json.load(open("params.json"))
pprint.pprint({'parameters': params})

data_type = params["general"]["data_type"]
subject_ids = params["general"]["subject_ids"]
NJOBS = params["general"]["NJOBS"]
if "data_path" in params["general"].keys():
    data_path = params["general"]["data_path"]
else:
    data_path = op.expanduser("~")
print("data_path : %s" % data_path)
```

--------------------------------

### Import necessary libraries for Ephypype connectivity analysis

Source: https://neuropycon.github.io/ephypype/_downloads/d3138d01de4953c0b0af80f10da863ea/plot_connectivity.ipynb

Imports essential libraries including os.path, numpy, nipype.pipeline.engine, and specific nodes and datasets from Ephypype. This setup is required before proceeding with connectivity computations.

```python
# Authors: Annalisa Pascarella <a.pascarella@iac.cnr.it>
# License: BSD (3-clause)

# sphinx_gallery_thumbnail_number = 2

import os.path as op
import numpy as np
import nipype.pipeline.engine as pe

import ephypype
from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.nodes import get_frequency_band
from ephypype.datasets import fetch_omega_dataset
```

--------------------------------

### Initialize Nipype workflow

Source: https://neuropycon.github.io/ephypype/_downloads/2c191d56a51323e1a46bf19ec940822c/plot_04-preprocessing_inverse.ipynb

Initializes a Nipype workflow named 'preprocessing_full_inverse' and sets its base directory for storing outputs. Ensure the specified `data_path` is accessible and has write permissions.

```python
# workflow directory within the `base_dir`
wf_name = 'preprocessing_full_inverse'
main_workflow = pe.Workflow(name=wf_name)
main_workflow.base_dir = data_path
```

--------------------------------

### Import necessary libraries for preprocessing

Source: https://neuropycon.github.io/ephypype/_downloads/156d56be1bfcb6a41fb0295d29f57e92/plot_preprocessing.ipynb

Imports nipype, ephypype modules, and utility functions for creating iterator and datagrabber nodes, as well as fetching datasets. This setup is required before defining the preprocessing workflow.

```python
# Authors: Annalisa Pascarella <a.pascarella@iac.cnr.it>
#          Mainak Jas <mainakjas@gmail.com>
# License: BSD (3-clause)

# sphinx_gallery_thumbnail_number = 2

import os.path as op

import nipype.pipeline.engine as pe

import ephypype
from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.datasets import fetch_omega_dataset
```

--------------------------------

### Import Libraries and Fetch Data

Source: https://neuropycon.github.io/ephypype/_downloads/28c69b982ff953f562e5d4eae4bc3c68/plot_power.ipynb

Imports necessary libraries and fetches the Omega dataset for analysis. Ensure the base path is correctly set.

```python
import os.path as op
import numpy as np
import nipype.pipeline.engine as pe

import ephypype
from ephypype.nodes import create_iterator, create_datagrabber
from ephypype.datasets import fetch_omega_dataset

base_path = op.join(op.dirname(ephypype.__file__), '..', 'examples')
data_path = fetch_omega_dataset(base_path)
```

--------------------------------

### Initialize Nipype Workflow

Source: https://neuropycon.github.io/ephypype/_downloads/9db9cdd4bbb411e68f83d88399605850/run_fieldtrip_wf.ipynb

Creates a nipype workflow engine instance and sets its base directory for storing outputs. This is a fundamental step in setting up any nipype-based analysis pipeline.

```python
workflow_name = 'time_frequency_analysis'

main_workflow = pe.Workflow(name=workflow_name)
main_workflow.base_dir = data_path
```

--------------------------------

### Get and Plot ERP Results

Source: https://neuropycon.github.io/ephypype/_downloads/50feaf72899c2174bc94bb258fca3e70/plot_ERP.ipynb

Retrieves computed evoked potential files using 'get_results' and then plots the Global Field Power (GFP) for different conditions (Faces, Car, Contrast) using MNE-Python.

```python
import mne  # noqa
import matplotlib.pyplot as plt  # noqa
from ephypype.gather import get_results  # noqa

evoked_files, _ = get_results(main_workflow.base_dir,
                              main_workflow.name, pipeline='compute_evoked')

for evoked_file in evoked_files:
    print(f'*** {evoked_file} ***\n')

    ave = mne.read_evokeds(evoked_file)
    faces, car = ave[0], ave[1]

    gfp_faces = faces.data.std(axis=0, ddof=0)
    gfp_car = car.data.std(axis=0, ddof=0)

    # compare conditions
    contrast = mne.combine_evoked([faces, car], weights=[1, -1])
    gfp_contrast = contrast.data.std(axis=0, ddof=0)

    # Reproducing the MNE-Python plot style seen above
    fig, ax = plt.subplots()
    ax.plot(faces.times, gfp_faces * 1e6, color='blue')
    ax.plot(car.times, gfp_car * 1e6, color='orange')
    ax.plot(contrast.times, gfp_contrast * 1e6, color='green')
    ax.legend(['Faces', 'Car', 'Contrast'])
    fig.show()
```

--------------------------------

### Import necessary libraries and fetch data

Source: https://neuropycon.github.io/ephypype/_sources/auto_examples/run_fieldtrip_IF.rst.txt

Imports required modules from ephypype and standard libraries. Fetches the iEEG dataset and loads parameters from a JSON file. This setup is necessary before applying the FieldTrip interface.

```python
# Authors: Annalisa Pascarella <a.pascarella@iac.cnr.it>
# License: BSD (3-clause)

import os.path as op

import ephypype
from ephypype.nodes.FT_tools import Reference
from ephypype.datasets import fetch_ieeg_dataset


base_path = op.join(op.dirname(ephypype.__file__), '..', 'examples')
data_path = fetch_ieeg_dataset(base_path)

import json  # noqa
import pprint  # noqa
params = json.load(open("params.json"))
pprint.pprint({'time frequency parameters': params["tfr"]})
ft_path = params["tfr"]['fieldtrip_path']
refmethod = params["tfr"]['refmethod']
channels_name = params["tfr"]['channels_name']
```

--------------------------------

### Create Preprocessing Pipeline Node

Source: https://neuropycon.github.io/ephypype/_downloads/d5151967f641f12ab39aa60c21fe976a/plot_eeg_preprocessing.ipynb

Instantiate the preprocessing pipeline node by calling `create_pipeline_preproc_meeg`. Pass necessary parameters such as data path, frequency filters, number of components, and channel names.

```python
preproc_workflow = create_pipeline_preproc_meeg(
    data_path, pipeline_name="preproc_eeg_pipeline",
    l_freq=l_freq, h_freq=h_freq, n_components=n_components, reject=reject,
    EoG_ch_name=EoG_ch_name, data_type=data_type, montage=montage,
    bipolar=bipolar, ch_new_names=ch_new_names)
```

--------------------------------

### Create MEEG Preprocessing Pipeline

Source: https://neuropycon.github.io/ephypype/_downloads/156d56be1bfcb6a41fb0295d29f57e92/plot_preprocessing.ipynb

Instantiate the MEEG preprocessing pipeline by importing the create_pipeline_preproc_meeg function and passing relevant parameters.

```python
from ephypype.pipelines import create_pipeline_preproc_meeg  # noqa
preproc_workflow = create_pipeline_preproc_meeg(
    data_path, l_freq=l_freq, h_freq=h_freq, down_sfreq=down_sfreq,
    variance=variance, ECG_ch_name=ECG_ch_name, EoG_ch_name=EoG_ch_name,
    data_type=data_type)
```

--------------------------------

### Fetch and Process iEEG Data with FieldTrip Reference

Source: https://neuropycon.github.io/ephypype/_sources/tutorials/wrap_fieldtrip.rst.txt

This snippet demonstrates fetching iEEG data and applying a bipolar rereferencing method using the FieldTrip Reference interface. Ensure FieldTrip is installed and its path is correctly set.

```python
import os.path as op
import ephypype
from ephypype.nodes.FT_tools import Reference
from ephypype.datasets import fetch_ieeg_dataset

base_path = op.join(op.dirname(ephypype.__file__), '..', 'examples')
data_path = fetch_ieeg_dataset(base_path)

ft_path = '/usr/local/MATLAB/R2018a/toolbox/MEEG/fieldtrip-20200327/'
refmethod = 'bipolar'
channels_name = '{"RAM*", "RHH*", "RTH*", "ROC*", "LAM*","LHH*", "LTH*"}'

reference_if = Reference()
reference_if.inputs.data_file = op.join(data_path, 'SubjectUCI29_data.mat')
reference_if.inputs.channels = channels_name
reference_if.inputs.ft_path = ft_path
reference_if.inputs.refmethod = refmethod
reference_if.inputs.script = ''

out = reference_if.run()

print('Rereferenced data saved at {}'.format(out.outputs.data_output))
```

--------------------------------

### Visualize and run the workflow

Source: https://neuropycon.github.io/ephypype/auto_examples/run_fieldtrip_wf.html

Generates a colored graph of the workflow, displays it using matplotlib, and then executes the workflow locally using the MultiProc plugin with 1 processor. It also configures the workflow to not remove unnecessary outputs.

```python
main_workflow.write_graph(graph2use='colored')  # colored

import matplotlib.pyplot as plt  # noqa
img = plt.imread(op.join(data_path, workflow_name, 'graph.png'))
plt.figure(figsize=(6, 6))
plt.imshow(img)
plt.axis('off')
main_workflow.write_graph(graph2use='colored')  # colored
main_workflow.config['execution'] = {'remove_unnecessary_outputs': 'false'}

# Run workflow locally on 1 CPU
main_workflow.run(plugin='MultiProc', plugin_args={'n_procs': 1})

```

--------------------------------

### Get and Inspect ICA Results

Source: https://neuropycon.github.io/ephypype/_sources/auto_workshop/01_meg/plot_01_meg_preprocessing.rst.txt

Retrieves ICA-processed files and raw data files from the workflow directory. It then iterates through these files, reads the raw MEG data and ICA decomposition, and plots the properties of the excluded ICA components.

```python
import mne  # noqa
from ephypype.gather import get_results # noqa

ica_files, raw_files = get_results(main_workflow.base_dir,
                                       main_workflow.name, pipeline='ica')

for ica_file, raw_file in zip(ica_files, raw_files):
    print(f'*** {raw_file} ***')
    raw = mne.io.read_raw_fif(raw_file)
    ica = mne.preprocessing.read_ica(ica_file)
    ica.plot_properties(raw, picks=ica.exclude, figsize=[4.5, 4.5])

    # ica.plot_components()
    # ica.plot_sources(raw)

```

--------------------------------

### Load and Plot ICA Properties

Source: https://neuropycon.github.io/ephypype/_downloads/156d56be1bfcb6a41fb0295d29f57e92/plot_preprocessing.ipynb

Loads raw data and ICA components using MNE-Python and plots the ICA properties for excluded components. Ensure MNE and Ephypype are installed and the workflow base directory and name are correctly specified.

```python
import mne  # noqa
from ephypype.gather import get_results  # noqa

ica_files, raw_files = get_results(main_workflow.base_dir,
                                   main_workflow.name, pipeline='ica')

for ica_file, raw_file in zip(ica_files, raw_files):
    raw = mne.io.read_raw_fif(raw_file)
    ica = mne.preprocessing.read_ica(ica_file)
    ica.plot_properties(raw, picks=ica.exclude, figsize=[4.5, 4.5])
```

--------------------------------

### Display Command Help

Source: https://neuropycon.github.io/ephypype/_sources/tutorial.rst.txt

Shows the help message for a specific command, detailing its options and arguments.

```bash
$ neuropycon ica --help
```

--------------------------------

### Create ReconAll Workflow

Source: https://neuropycon.github.io/ephypype/_downloads/12023be1642091db1234b133c6d54fe8/01-run-smri_reconall.ipynb

Sets up the reconall_workflow, specifying its base directory and connecting the infosource, datasource, and recon_all nodes. This workflow handles the initial segmentation of structural data.

```python
# reconall_workflow will be a node of the main workflow
reconall_workflow_name = 'segmentation_workflow'
reconall_workflow = pe.Workflow(name=reconall_workflow_name)
reconall_workflow.base_dir = data_path

reconall_workflow.connect(infosource, 'subject_id', datasource,  'subject_id')
reconall_workflow.connect(infosource, 'subject_id', recon_all, 'subject_id')
reconall_workflow.connect(datasource, 'raw_file', recon_all, 'T1_files')
```

--------------------------------

### Import Libraries and Fetch Data

Source: https://neuropycon.github.io/ephypype/_downloads/1a926fb439cbc5d0c73fd5013ba067ba/plot_inverse_LCMV.ipynb

Imports necessary libraries and fetches the omega dataset. This is a prerequisite for running the source reconstruction pipeline.

```python
# Authors: Annalisa Pascarella <a.pascarella@iac.cnr.it>
# License: BSD (3-clause)

# sphinx_gallery_thumbnail_number = 2

import os.path as op
import numpy as np
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio

import ephypype
from ephypype.nodes import create_iterator
from ephypype.datasets import fetch_omega_dataset

data_type = 'fif'
base_path = op.join(op.dirname(ephypype.__file__), '..', 'examples')
data_path = fetch_omega_dataset(base_path)
```

--------------------------------

### Initialize Nipype Workflow

Source: https://neuropycon.github.io/ephypype/_downloads/28c69b982ff953f562e5d4eae4bc3c68/plot_power.ipynb

Creates a Nipype workflow and sets its base directory for storing outputs. The workflow name is specified for organization.

```python
# workflow directory within the `base_dir`
power_analysis_name = 'power_workflow'

main_workflow = pe.Workflow(name=power_analysis_name)
main_workflow.base_dir = data_path
```
Tokens:
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