Add example plot_fmri_stats_map.py

Author: sheyma

examples/eeg_meg/plot_fmri_stats_map.py

@@ -0,0 +1,78 @@
+"""
+Display a volumetric fmri-stats map across the brain surface
+=============================================================
+
+This example script does the following:
+  1) Download a nifti file from nilearn data set
+  2) Resample it on visbrain BrainObj
+  3) Plot it in a thresholded fashion
+
+Inspired by nilearn.plotting.plot_surf_stat_map
+
+"""
+
+from visbrain.objects import BrainObj, ColorbarObj, SceneObj
+from nilearn import datasets, surface
+
+sc = SceneObj(bgcolor='black', size=(1000, 500))
+
+# Colorbar default arguments
+CBAR_STATE = dict(cbtxtsz=20, txtsz=20., width=.1, cbtxtsh=3.,
+                  rect=(-.3, -2., 1., 4.))
+KW = dict(title_size=14., zoom=1.2)
+
+motor_images = datasets.fetch_neurovault_motor_task()
+stat_img     = motor_images.images[0]
+# stat_img is a nifti file: "image_10426.nii.gz"
+
+b_obj = BrainObj('white',
+                 translucent=False)
+
+mesh  = [b_obj.vertices, b_obj.faces]
+
+# resample from nifti to mesh
+texture = surface.vol_to_surf(stat_img, mesh)
+
+# plot mesh across brain oject
+b_obj.add_activation(-1 * texture,
+                     cmap='Blues_r',
+                     clim=(1, 7.9),
+                     vmin=1,
+                     vmax=7.9,
+                     hide_under=1,)
+
+cb_proj = ColorbarObj(b_obj,
+                      cblabel='stats map (-)',
+                      cmap='Blues',
+                      vmin=-7.9,
+                      vmax=-1,
+                      clim=(-7.9, -1),
+                      #over='gainsboro',
+                      **CBAR_STATE)
+
+b_obj.add_activation(texture,
+                     cmap='Reds_r',
+                     vmin=1,
+                     vmax=7.9,
+                     clim=(1, 7.9),
+                     hide_under=1)
+
+cb_proj_2 = ColorbarObj(b_obj,
+                      cblabel='statsmap (+)',
+                      cmap='Reds_r',
+                      vmin = 1,
+                      vmax=7.9,
+                      #under='gainsboro',
+                      **CBAR_STATE)
+
+sc.add_to_subplot(b_obj, row=0, col=0, rotate='right')
+
+sc.add_to_subplot(cb_proj,
+                  row=0, col=1,
+                  width_max=200)
+
+sc.add_to_subplot(cb_proj_2,
+                  row=0, col=2,
+                  width_max=200)
+
+sc.preview()