Visualizing Nifti Files

Function Name	Function Description
plot_anat	Plotting an anatomical image
plot_glass_brain	Glass brain visualization. By default plots maximum intensity projection of the absolute values. To plot positive and negative values set plot_abs parameter to False.
plot_img	General-purpose function, with no specific presets
plot_stat_map	Plotting a statistical map, like a T-map, a Z-map, or an ICA, with an optional background
plot_epi	Plotting an EPI, or T2* image
plot_surf_roi	Plotting surface atlases on a brain surface

                                        
        1. Basic Atlas plotting

                from nilearn import datasets

                dataset = datasets.fetch_atlas_harvard_oxford('cort-maxprob-thr25-2mm')
                atlas_filename = dataset.maps
                print('Atlas ROIs are located at: %s' % atlas_filename)

                from nilearn import plotting

                plotting.plot_roi(atlas_filename, title="Harvard Oxford atlas")
                plotting.show()

        2. Glass brain plotting in nilearn    

                from nilearn import datasets

                motor_images = datasets.fetch_neurovault_motor_task()
                stat_img = motor_images.images[0]

                plotting.plot_glass_brain(stat_img, title='plot_glass_brain',black_bg=True, display_mode='xz', threshold=3)

                plotting.plot_glass_brain(stat_img,
                          title='plot_glass_brain with display_mode="lyrz"',
                          display_mode='lyrz', threshold=3)

                plotting.show()

        3. Making a surface plot of a 3D statistical map

                from nilearn import datasets

                motor_images = datasets.fetch_neurovault_motor_task()
                stat_img = motor_images.images[0]

                fsaverage = datasets.fetch_surf_fsaverage()

                from nilearn import surface

                texture = surface.vol_to_surf(stat_img, fsaverage.pial_right)

                from nilearn import plotting

                plotting.plot_surf_stat_map(fsaverage.infl_right, texture, hemi='right',
                            title='Surface right hemisphere', colorbar=True,
                            threshold=1., bg_map=fsaverage.sulc_right)

                plotting.plot_glass_brain(stat_img, display_mode='r', plot_abs=False,
                            title='Glass brain', threshold=2.)
  
                plotting.plot_stat_map(stat_img, display_mode='x', threshold=1.,
                         cut_coords=range(0, 51, 10), title='Slices')

1. Basic Atlas plotting	2. Glass brain plotting in nilearn	3. Making a surface plot of a 3D statistical map

Visualisation of Nifti Files

Plotting functions in nilearn