.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/06_manipulating_images/plot_nifti_simple.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note Click :ref:`here ` to download the full example code or to run this example in your browser via Binder .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_06_manipulating_images_plot_nifti_simple.py: Simple example of NiftiMasker use ================================== Here is a simple example of automatic mask computation using the nifti masker. The mask is computed and visualized. .. GENERATED FROM PYTHON SOURCE LINES 10-11 Retrieve the brain development functional dataset .. GENERATED FROM PYTHON SOURCE LINES 11-19 .. code-block:: default from nilearn import datasets dataset = datasets.fetch_development_fmri(n_subjects=1) func_filename = dataset.func[0] # print basic information on the dataset print('First functional nifti image (4D) is at: %s' % func_filename) .. rst-class:: sphx-glr-script-out Out: .. code-block:: none First functional nifti image (4D) is at: /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz .. GENERATED FROM PYTHON SOURCE LINES 20-21 Compute the mask .. GENERATED FROM PYTHON SOURCE LINES 21-32 .. code-block:: default from nilearn.maskers import NiftiMasker # As this is raw movie watching based EPI, the background is noisy and we # cannot rely on the 'background' masking strategy. We need to use the 'epi' # one nifti_masker = NiftiMasker(standardize=True, mask_strategy='epi', memory="nilearn_cache", memory_level=2, smoothing_fwhm=8) nifti_masker.fit(func_filename) mask_img = nifti_masker.mask_img_ .. GENERATED FROM PYTHON SOURCE LINES 33-34 Visualize the mask using the plot_roi method .. GENERATED FROM PYTHON SOURCE LINES 34-42 .. code-block:: default from nilearn.plotting import plot_roi from nilearn.image.image import mean_img # calculate mean image for the background mean_func_img = mean_img(func_filename) plot_roi(mask_img, mean_func_img, display_mode='y', cut_coords=4, title="Mask") .. image-sg:: /auto_examples/06_manipulating_images/images/sphx_glr_plot_nifti_simple_001.png :alt: plot nifti simple :srcset: /auto_examples/06_manipulating_images/images/sphx_glr_plot_nifti_simple_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 43-47 Visualize the mask using the 'generate_report' method This report can be displayed in a Jupyter Notebook, opened in-browser using the .open_in_browser() method, or saved to a file using the .save_as_html(output_filepath) method. .. GENERATED FROM PYTHON SOURCE LINES 47-50 .. code-block:: default report = nifti_masker.generate_report() report .. raw:: html

NiftiMasker Applying a mask to extract time-series from Niimg-like objects. NiftiMasker is useful when preprocessing (detrending, standardization, resampling, etc.) of in-mask :term:`voxels<voxel>` is necessary. Use case: working with time series of resting-state or task maps.

image

This report shows the input Nifti image overlaid with the outlines of the mask (in green). We recommend to inspect the report for the overlap between the mask and its input image.

Parameters
Parameter Value
detrend False
dtype None
high_pass None
high_variance_confounds False
low_pass None
mask_args None
mask_img None
mask_strategy epi
memory Memory(location=nilearn_cache/joblib)
memory_level 2
reports True
runs None
smoothing_fwhm 8
standardize True
standardize_confounds True
t_r None
target_affine None
target_shape None
verbose 0


.. GENERATED FROM PYTHON SOURCE LINES 51-52 Preprocess data with the NiftiMasker .. GENERATED FROM PYTHON SOURCE LINES 52-56 .. code-block:: default nifti_masker.fit(func_filename) fmri_masked = nifti_masker.transform(func_filename) # fmri_masked is now a 2D matrix, (n_voxels x n_time_points) .. GENERATED FROM PYTHON SOURCE LINES 57-58 Run an algorithm .. GENERATED FROM PYTHON SOURCE LINES 58-63 .. code-block:: default from sklearn.decomposition import FastICA n_components = 10 ica = FastICA(n_components=n_components, random_state=42) components_masked = ica.fit_transform(fmri_masked.T).T .. rst-class:: sphx-glr-script-out Out: .. code-block:: none /home/nicolas/GitRepos/scikit-learn-fork/sklearn/decomposition/_fastica.py:484: FutureWarning: From version 1.3 whiten='unit-variance' will be used by default. /home/nicolas/GitRepos/scikit-learn-fork/sklearn/decomposition/_fastica.py:116: ConvergenceWarning: FastICA did not converge. Consider increasing tolerance or the maximum number of iterations. .. GENERATED FROM PYTHON SOURCE LINES 64-65 Reverse masking, and display the corresponding map .. GENERATED FROM PYTHON SOURCE LINES 65-79 .. code-block:: default components = nifti_masker.inverse_transform(components_masked) # Visualize results from nilearn.plotting import plot_stat_map, show from nilearn.image import index_img from nilearn.image.image import mean_img # calculate mean image for the background mean_func_img = mean_img(func_filename) plot_stat_map(index_img(components, 0), mean_func_img, display_mode='y', cut_coords=4, title="Component 0") show() .. image-sg:: /auto_examples/06_manipulating_images/images/sphx_glr_plot_nifti_simple_002.png :alt: plot nifti simple :srcset: /auto_examples/06_manipulating_images/images/sphx_glr_plot_nifti_simple_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 17.078 seconds) **Estimated memory usage:** 387 MB .. _sphx_glr_download_auto_examples_06_manipulating_images_plot_nifti_simple.py: .. only :: html .. container:: sphx-glr-footer :class: sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://mybinder.org/v2/gh/nilearn/nilearn.github.io/main?filepath=examples/auto_examples/06_manipulating_images/plot_nifti_simple.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_nifti_simple.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_nifti_simple.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_