"""
Intro to GLM Analysis: a single-run, single-subject fMRI dataset
================================================================

In this tutorial, we use a General Linear Model (:term:`GLM`) to compare the
:term:`fMRI` signal during periods of auditory stimulation
versus periods of rest.

.. warning::

    The analysis described here is performed in the native space,
    directly on the original :term:`EPI` scans
    without any spatial or temporal preprocessing.
    More sensitive results would likely be obtained on the corrected,
    spatially normalized and smoothed images.
"""
# %%
# Retrieving the data
# -------------------
#
# .. note:: In this tutorial, we load the data using a data downloading
#           function. To input your own data, you will need to provide
#           a list of paths to your own files in the ``subject_data`` variable.
#           These should abide to the Brain Imaging Data Structure
#           (:term:`BIDS`) organization.

from nilearn.datasets import fetch_spm_auditory

subject_data = fetch_spm_auditory()

# %%
# Inspecting the dataset
# ----------------------

# %%
# print paths of func image
subject_data.func[0]

# %%
# We can display the mean functional image and the subject's anatomy:
from nilearn.image import mean_img
from nilearn.plotting import plot_anat, plot_img, plot_stat_map, show

fmri_img = subject_data.func
mean_img = mean_img(subject_data.func[0], copy_header=True)
plot_img(mean_img, cbar_tick_format="%i")

plot_anat(subject_data.anat, cbar_tick_format="%i")

show()


# %%
# Specifying the experimental paradigm
# ------------------------------------
#
# We must now provide a description of the experiment, that is,
# define the timing of the auditory stimulation and rest periods.
# This is typically provided in an events.tsv file.
# The path of this file is provided in the dataset.
import pandas as pd

events = pd.read_table(subject_data.events)
events


# %%
# Performing the :term:`GLM` analysis
# -----------------------------------
#
# It is now time to create and estimate a ``FirstLevelModel`` object,
# that will generate the *design matrix*
# using the information provided by the ``events`` object.

from nilearn.glm.first_level import FirstLevelModel

# %%
# Parameters of the first-level model
#
# * ``t_r=7(s)`` is the time of repetition of acquisitions
# * ``noise_model='ar1'`` specifies the noise covariance model:
#   a lag-1 dependence
# * ``standardize=False`` means that we do not want
#   to rescale the time series to mean 0, variance 1
# * ``hrf_model='spm'`` means that we rely
#   on the :term:`SPM` "canonical hrf" model
#   (without time or dispersion derivatives)
# * ``drift_model='cosine'`` means that we model the signal drifts
#   as slow oscillating time functions
# * ``high_pass=0.01`` (Hz) defines the cutoff frequency
#   (inverse of the time period).
fmri_glm = FirstLevelModel(
    t_r=7,
    noise_model="ar1",
    standardize=False,
    hrf_model="spm",
    drift_model="cosine",
    high_pass=0.01,
)

# %%
# Now that we have specified the model, we can run it on the :term:`fMRI` image
fmri_glm = fmri_glm.fit(fmri_img, events)

# %%
# One can inspect the design matrix (rows represent time, and
# columns contain the predictors).
design_matrix = fmri_glm.design_matrices_[0]

# %%
# Formally, we have taken the first design matrix, because the model is
# implictily meant to for multiple runs.
from nilearn.plotting import plot_design_matrix

plot_design_matrix(design_matrix)

show()

# %%
# Save the design matrix image to disk
# first create a directory where you want to write the images
from pathlib import Path

output_dir = Path.cwd() / "results" / "plot_single_subject_single_run"
output_dir.mkdir(exist_ok=True, parents=True)
print(f"Output will be saved to: {output_dir}")

plot_design_matrix(design_matrix, output_file=output_dir / "design_matrix.png")

# %%
# The first column contains the expected response profile of regions which are
# sensitive to the auditory stimulation.
# Let's plot this first column
import matplotlib.pyplot as plt

plt.plot(design_matrix["listening"])
plt.xlabel("scan")
plt.title("Expected Auditory Response")

show()


# %%
# Detecting voxels with significant effects
# -----------------------------------------
#
# To access the estimated coefficients (Betas of the :term:`GLM` model),
# we created :term:`contrast` with a single '1' in each of the columns:
# The role of the :term:`contrast` is to select some columns of the model
# --and potentially weight them-- to study the associated statistics.
# So in a nutshell, a :term:`contrast`
# is a weighted combination of the estimated effects.
# Here we can define canonical contrasts that just consider
# the effect of the stimulation in isolation.
#
# .. note::
#
#       Here the baseline is implicit, so passing a value of 1
#       for the first column will give contrast for: ``listening > rest``
#

import numpy as np

n_regressors = design_matrix.shape[1]
activation = np.zeros(n_regressors)
activation[0] = 1

# %%
# Let's look at it: plot the coefficients of the :term:`contrast`,
# indexed by the names of the columns of the design matrix.

from nilearn.plotting import plot_contrast_matrix

plot_contrast_matrix(contrast_def=activation, design_matrix=design_matrix)

# %%
# Below, we compute the :term:`'estimated effect'<Parameter Estimate>`.
# It is in :term:`BOLD` signal unit, but has no statistical guarantees,
# because it does not take into account the associated variance.

eff_map = fmri_glm.compute_contrast(activation, output_type="effect_size")

# %%
# In order to get statistical significance, we form a t-statistic, and
# directly convert it into z-scale. The z-scale means that the values
# are scaled to match a standard Gaussian distribution (mean=0,
# variance=1), across voxels, if there were no effects in the data.

z_map = fmri_glm.compute_contrast(activation, output_type="z_score")


# %%
# Plot thresholded z scores map
# -----------------------------
#
# We display it on top of the average functional image of the series
# (could be the anatomical image of the subject).
# We use arbitrarily a threshold of 3.0 in z-scale.
# We'll see later how to use corrected thresholds.
# We will show 3 axial views, with display_mode='z' and cut_coords=3.
plotting_config = {
    "bg_img": mean_img,
    "display_mode": "z",
    "cut_coords": 3,
    "black_bg": True,
}
plot_stat_map(
    z_map,
    threshold=3,
    title="listening > rest (|Z|>3)",
    figure=plt.figure(figsize=(10, 4)),
    **plotting_config,
)
show()

# %%
# .. note::
#
#   Notice how the visualizations above shows both 'activated' voxels
#   with Z > 3,
#   as well as 'deactivated' voxels with Z < -3.
#   In the rest of this example we will show only the activate voxels
#   by using one-sided tests.

# %%
# Statistical significance testing
# --------------------------------
#
# One should worry about the statistical validity of the procedure:
# here we used an arbitrary
# threshold of 3.0 but the threshold should provide some guarantees on
# the risk of false detections (aka type-1 errors in statistics).
# One suggestion is to control the false positive rate
# (:term:`fpr<FPR correction>`, denoted by alpha)
# at a certain level, e.g. 0.001: this means that there is 0.1% chance
# of declaring an inactive :term:`voxel`, active.

from nilearn.glm import threshold_stats_img

clean_map, threshold = threshold_stats_img(
    z_map,
    alpha=0.001,
    height_control="fpr",
    two_sided=False,  # using a one-sided test
)
# Let's use a sequential colormap as we will only display positive values.
plotting_config["cmap"] = "inferno"
plot_stat_map(
    clean_map,
    threshold=threshold,
    title=(
        f"listening > rest (Uncorrected p<0.001; threshold: {threshold:.3f})"
    ),
    figure=plt.figure(figsize=(10, 4)),
    **plotting_config,
)
show()

# %%
# The problem is that with this you expect 0.001 * n_voxels to show up
# while they're not active --- tens to hundreds of voxels. A more
# conservative solution is to control the family wise error rate,
# i.e. the probability of making only one false detection, say at
# 5%. For that we use the so-called Bonferroni correction.

clean_map, threshold = threshold_stats_img(
    z_map, alpha=0.05, height_control="bonferroni", two_sided=False
)
plot_stat_map(
    clean_map,
    threshold=threshold,
    title=(
        "listening > rest (p<0.05 Bonferroni-corrected, "
        f"threshold: {threshold:.3f})"
    ),
    figure=plt.figure(figsize=(10, 4)),
    **plotting_config,
)
show()

# %%
# This is quite conservative indeed!  A popular alternative is to
# control the expected proportion of
# false discoveries among detections. This is called the False
# discovery rate.

clean_map, threshold = threshold_stats_img(
    z_map, alpha=0.05, height_control="fdr", two_sided=False
)
plot_stat_map(
    clean_map,
    threshold=threshold,
    title=(
        f"listening > rest (p<0.05 FDR-corrected; threshold: {threshold:.3f})"
    ),
    figure=plt.figure(figsize=(10, 4)),
    **plotting_config,
)
show()

# %%
# Finally people like to discard isolated voxels (aka "small
# clusters") from these images. It is possible to generate a
# thresholded map with small clusters removed by providing a
# cluster_threshold argument. Here clusters smaller than 10 voxels
# will be discarded.

clean_map, threshold = threshold_stats_img(
    z_map,
    alpha=0.05,
    height_control="fdr",
    cluster_threshold=10,
    two_sided=False,
)
plot_stat_map(
    clean_map,
    threshold=threshold,
    title=(
        "listening > rest "
        f"(p<0.05 FDR-corrected; threshold: {threshold:.3f}; "
        "clusters > 10 voxels)"
    ),
    figure=plt.figure(figsize=(10, 4)),
    **plotting_config,
)
show()


# %%
# We can save the effect and zscore maps to the disk.
z_map.to_filename(output_dir / "listening_gt_rest_z_map.nii.gz")
eff_map.to_filename(output_dir / "listening_gt_rest_eff_map.nii.gz")

# %%
# We can furthermore extract and report the found positions in a table.
#
# .. seealso::
#
#     This function does not report any named anatomical location
#     for the clusters.
#     To get the names of the location of the clusters
#     according to one or several atlases,
#     we recommend using
#     the `atlasreader package <https://github.com/miykael/atlasreader>`_.
#
from nilearn.reporting import get_clusters_table

table = get_clusters_table(
    z_map, stat_threshold=threshold, cluster_threshold=20
)
table

# %%
# This table can be saved for future use.

table.to_csv(output_dir / "table.csv")

# %%
# Performing an F-test
# --------------------
#
# "listening > rest" is a typical t test: condition versus baseline.
# Another popular type of test is an F test in which
# one seeks whether a certain combination of conditions
# (possibly two-, three- or higher-dimensional)
# explains a significant proportion of the signal.
# Here one might for instance test which voxels are well
# explained by the combination of more active or less active than rest.
#
# .. note::
#
#    As opposed to t-tests, the beta images produced by of F-tests
#    only contain positive values.
#

# %%
# Specify the :term:`contrast` and compute the corresponding map.
# Actually, the :term:`contrast` specification is done exactly the same way
# as for t-contrasts.

z_map = fmri_glm.compute_contrast(
    activation,
    output_type="z_score",
    stat_type="F",  # set stat_type to 'F' to perform an F test
)

# %%
# Note that the statistic has been converted to a z-variable,
# which makes it easier to represent it.

clean_map, threshold = threshold_stats_img(
    z_map,
    alpha=0.05,
    height_control="fdr",
    cluster_threshold=10,
    two_sided=False,
)
plot_stat_map(
    clean_map,
    threshold=threshold,
    title="Effects of interest (fdr=0.05), clusters > 10 voxels",
    figure=plt.figure(figsize=(10, 4)),
    **plotting_config,
)
show()
