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---

# Multi-Echo Denoising with `tedana`

In this analysis tutorial, we will use `tedana` {cite:p}`DuPre2021` to perform multi-echo denoising.

Specifically, we will use {py:func}`tedana.workflows.tedana_workflow`.

```{code-cell} ipython3
import json
import os
from glob import glob
from pprint import pprint

import nibabel as nb
import pandas as pd
from IPython.display import HTML, display
from book_utils import load_pafin
from tedana import workflows

data_path = os.path.abspath('../data')
```

```{code-cell} ipython3
data = load_pafin(data_path)
out_dir = os.path.join(data_path, "tedana")
```

```{code-cell} ipython3
:tags: [hide-output]

workflows.tedana_workflow(
    data['echo_files'],
    data['echo_times'],
    out_dir=out_dir,
    mask=data['mask'],
    prefix="sub-24053_ses-1_task-rat_dir-PA_run-01",
    fittype="loglin",
    tedpca="mdl",
    verbose=True,
    gscontrol=["mir"],
    overwrite=True,
)
```

The tedana workflow writes out a number of files.

```{code-cell} ipython3
out_files = sorted(glob(os.path.join(out_dir, "*")))
out_files = [os.path.basename(f) for f in out_files]
print("\n".join(out_files))
```

```{code-cell} ipython3
metrics = pd.read_table(
    os.path.join(out_dir, "sub-24053_ses-1_task-rat_dir-PA_run-01_desc-tedana_metrics.tsv")
)
```

```{code-cell} ipython3
:tags: [hide-input]
def color_rejected_red(series):
    """Color rejected components red."""
    return [
        "color: red" if series["classification"] == "rejected" else "" for v in series
    ]


metrics.style.apply(color_rejected_red, axis=1)
```

```{code-cell} ipython3
with open(
    os.path.join(out_dir, "sub-24053_ses-1_task-rat_dir-PA_run-01_desc-tedana_metrics.json"),
    "r",
) as fo:
    metrics = json.load(fo)

first_five_keys = list(metrics.keys())[:5]
reduced_metrics = {k: metrics[k] for k in first_five_keys}
pprint(reduced_metrics)
```

```{code-cell} ipython3
:tags: [output_scroll]

df = pd.DataFrame.from_dict(metrics, orient="index")
df = df.fillna("n/a")
display(HTML(df.to_html()))
```

```{code-cell} ipython3
report = os.path.join(out_dir, "sub-24053_ses-1_task-rat_dir-PA_run-01_tedana_report.html")
with open(report, "r") as fo:
    report_data = fo.read()

figures_dir = os.path.relpath(os.path.join(out_dir, "figures"), os.getcwd())
report_data = report_data.replace("./figures", figures_dir)

display(HTML(report_data))
```