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[DOC] Fix rendering of explanatory text #3972

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Sep 14, 2023
Merged

[DOC] Fix rendering of explanatory text #3972

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30 changes: 15 additions & 15 deletions examples/06_manipulating_images/plot_mask_computation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,9 @@

"""

###############################################################################
# %%
# Computing a mask from the background
###############################################################################
# ------------------------------------
#
# The default strategy to compute a mask, eg in NiftiMasker is to try to
# detect the background.
Expand All @@ -44,7 +44,7 @@
miyawaki_filename = miyawaki_dataset.func[0]
miyawaki_mean_img = image.mean_img(miyawaki_filename)
plot_epi(miyawaki_mean_img, title="Mean EPI image")
###############################################################################
# %%
# A NiftiMasker with the default strategy
masker = NiftiMasker()
masker.fit(miyawaki_filename)
Expand All @@ -54,15 +54,15 @@
masker.mask_img_, miyawaki_mean_img, title="Mask from already masked data"
)

###############################################################################
# %%
# Plot the generated mask using the .generate_report method
report = masker.generate_report()
report


###############################################################################
# %%
# Computing a mask from raw EPI data
###############################################################################
# ----------------------------------
#
# From raw EPI data, there is no uniform background, and a different
# strategy is necessary
Expand All @@ -80,15 +80,15 @@
mean_img = image.mean_img(epi_img)
plot_epi(mean_img, title="Mean EPI image")

###############################################################################
# %%
# Simple mask extraction from EPI images
# We need to specify an 'epi' mask_strategy, as this is raw EPI data
masker = NiftiMasker(mask_strategy="epi")
masker.fit(epi_img)
report = masker.generate_report()
report

###############################################################################
# %%
# Generate mask with strong opening
#
# We can fine-tune the outline of the mask by increasing the number of
Expand All @@ -102,7 +102,7 @@
report = masker.generate_report()
report

###############################################################################
# %%
# Generate mask with a high lower cutoff
#
# The NiftiMasker calls the nilearn.masking.compute_epi_mask function to
Expand All @@ -121,9 +121,9 @@
report = masker.generate_report()
report

###############################################################################
# %%
# Computing the mask from the MNI template
###############################################################################
# ----------------------------------------
#
# A mask can also be computed from the MNI template. In this case, it is
# resampled to the target image. Three options are available:
Expand All @@ -135,9 +135,9 @@
report = masker.generate_report()
report

###############################################################################
# %%
# Compute and resample a mask
###############################################################################
# ---------------------------
#
# NiftiMasker also allows passing parameters directly to `image.resample_img`.
# We can specify a `target_affine`, a `target_shape`, or both.
Expand All @@ -154,9 +154,9 @@
report = masker.generate_report()
report

###############################################################################
# %%
# After mask computation: extracting time series
###############################################################################
# ----------------------------------------------
#
# Extract time series

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