.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/plot_3d_and_4d_niimg.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_plot_3d_and_4d_niimg.py: 3D and 4D niimgs: handling and visualizing ========================================== Here we discover how to work with 3D and 4D niimgs. .. GENERATED FROM PYTHON SOURCE LINES 9-15 Downloading tutorial datasets from Internet -------------------------------------------- Nilearn comes with functions that download public data from Internet Let's first check where the data is downloaded on our disk: .. GENERATED FROM PYTHON SOURCE LINES 15-18 .. code-block:: default from nilearn import datasets print('Datasets are stored in: %r' % datasets.get_data_dirs()) .. rst-class:: sphx-glr-script-out Out: .. code-block:: none Datasets are stored in: ['/home/nicolas/nilearn_data'] .. GENERATED FROM PYTHON SOURCE LINES 19-20 Let's now retrieve a motor contrast from a Neurovault repository .. GENERATED FROM PYTHON SOURCE LINES 20-23 .. code-block:: default motor_images = datasets.fetch_neurovault_motor_task() motor_images.images .. rst-class:: sphx-glr-script-out Out: .. code-block:: none ['/home/nicolas/nilearn_data/neurovault/collection_658/image_10426.nii.gz'] .. GENERATED FROM PYTHON SOURCE LINES 24-25 motor_images is a list of filenames. We need to take the first one .. GENERATED FROM PYTHON SOURCE LINES 25-28 .. code-block:: default tmap_filename = motor_images.images[0] .. GENERATED FROM PYTHON SOURCE LINES 29-34 Visualizing a 3D file ---------------------- The file contains a 3D volume, we can easily visualize it as a statistical map: .. GENERATED FROM PYTHON SOURCE LINES 34-37 .. code-block:: default from nilearn import plotting plotting.plot_stat_map(tmap_filename) .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_001.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none /home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/img_plotting.py:300: FutureWarning: Default resolution of the MNI template will change from 2mm to 1mm in version 0.10.0 anat_img = load_mni152_template() .. GENERATED FROM PYTHON SOURCE LINES 38-39 Visualizing works better with a threshold .. GENERATED FROM PYTHON SOURCE LINES 39-42 .. code-block:: default plotting.plot_stat_map(tmap_filename, threshold=3) .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_002.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 43-48 Visualizing one volume in a 4D file ----------------------------------- We can download resting-state networks from the Smith 2009 study on correspondence between rest and task .. GENERATED FROM PYTHON SOURCE LINES 48-51 .. code-block:: default rsn = datasets.fetch_atlas_smith_2009()['rsn10'] rsn .. rst-class:: sphx-glr-script-out Out: .. code-block:: none '/home/nicolas/nilearn_data/smith_2009/PNAS_Smith09_rsn10.nii.gz' .. GENERATED FROM PYTHON SOURCE LINES 52-54 It is a 4D nifti file. We load it into the memory to print its shape. .. GENERATED FROM PYTHON SOURCE LINES 54-57 .. code-block:: default from nilearn import image print(image.load_img(rsn).shape) .. rst-class:: sphx-glr-script-out Out: .. code-block:: none (91, 109, 91, 10) .. GENERATED FROM PYTHON SOURCE LINES 58-59 We can retrieve the first volume (note that Python indexing starts at 0): .. GENERATED FROM PYTHON SOURCE LINES 59-62 .. code-block:: default first_rsn = image.index_img(rsn, 0) print(first_rsn.shape) .. rst-class:: sphx-glr-script-out Out: .. code-block:: none (91, 109, 91) .. GENERATED FROM PYTHON SOURCE LINES 63-66 first_rsn is a 3D image. We can then plot it .. GENERATED FROM PYTHON SOURCE LINES 66-69 .. code-block:: default plotting.plot_stat_map(first_rsn) .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_003.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 70-78 Looping on all volumes in a 4D file ----------------------------------- If we want to plot all the volumes in this 4D file, we can use iter_img to loop on them. Then we give a few arguments to plot_stat_map in order to have a more compact display. .. GENERATED FROM PYTHON SOURCE LINES 78-84 .. code-block:: default for img in image.iter_img(rsn): # img is now an in-memory 3D img plotting.plot_stat_map(img, threshold=3, display_mode="z", cut_coords=1, colorbar=False) .. rst-class:: sphx-glr-horizontal * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_004.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_004.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_005.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_005.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_006.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_006.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_007.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_007.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_008.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_008.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_009.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_009.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_010.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_010.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_011.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_011.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_012.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_012.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_013.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_013.png :class: sphx-glr-multi-img .. GENERATED FROM PYTHON SOURCE LINES 85-93 Looping through selected volumes in a 4D file --------------------------------------------- If we want to plot selected volumes in this 4D file, we can use index_img with the `slice` constructor to select the desired volumes. Afterwards, we'll use iter_img to loop through them following the same formula as before. .. GENERATED FROM PYTHON SOURCE LINES 93-95 .. code-block:: default selected_volumes = image.index_img(rsn, slice(3, 5)) .. GENERATED FROM PYTHON SOURCE LINES 96-99 If you're new to Python, one thing to note is that the slice constructor uses 0-based indexing. You can confirm this by matching these slices to the previous plot above. .. GENERATED FROM PYTHON SOURCE LINES 99-104 .. code-block:: default for img in image.iter_img(selected_volumes): plotting.plot_stat_map(img) .. rst-class:: sphx-glr-horizontal * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_014.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_014.png :class: sphx-glr-multi-img * .. image-sg:: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_015.png :alt: plot 3d and 4d niimg :srcset: /auto_examples/images/sphx_glr_plot_3d_and_4d_niimg_015.png :class: sphx-glr-multi-img .. GENERATED FROM PYTHON SOURCE LINES 105-107 plotting.show is useful to force the display of figures when running outside IPython .. GENERATED FROM PYTHON SOURCE LINES 107-109 .. code-block:: default plotting.show() .. GENERATED FROM PYTHON SOURCE LINES 110-128 | ______ To recap, neuroimaging images (niimgs as we call them) come in different flavors: * 3D images, containing only one brain volume * 4D images, containing multiple brain volumes. More details about the input formats in nilearn for 3D and 4D images is given in the documentation section: :ref:`loading_data`. Functions accept either 3D or 4D images, and we need to use on the one hand :func:`nilearn.image.index_img` or :func:`nilearn.image.iter_img` to break down 4D images into 3D images, and on the other hand :func:`nilearn.image.concat_imgs` to group a list of 3D images into a 4D image. .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 15.346 seconds) **Estimated memory usage:** 127 MB .. _sphx_glr_download_auto_examples_plot_3d_and_4d_niimg.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/plot_3d_and_4d_niimg.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_3d_and_4d_niimg.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_3d_and_4d_niimg.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_