Resample an image to a template#

The goal of this example is to illustrate the use of the function nilearn.image.resample_to_img to resample an image to a template. We use the MNI152 template as the reference for resampling a t-map image. Function nilearn.image.resample_img could also be used to achieve this.

First we load the required datasets using the nilearn datasets module.

Now, the motor contrast map image can be resampled to the MNI template image.

Let’s check the shape and affine have been correctly updated.

# First load the original t-map in memory:
from nilearn.image import load_img

tmap_img = load_img(stat_img)

original_shape = tmap_img.shape
original_affine = tmap_img.affine

resampled_shape = resampled_stat_img.shape
resampled_affine = resampled_stat_img.affine

template_img = load_img(template)
template_shape = template_img.shape
template_affine = template_img.affine
print(
    f"""Shape comparison:
- Original t-map image shape : {original_shape}
- Resampled t-map image shape: {resampled_shape}
- Template image shape       : {template_shape}
"""
)

print(
    f"""Affine comparison:
- Original t-map image affine :
 {original_affine}
- Resampled t-map image affine:
 {resampled_affine}
- Template image affine       :
 {template_affine}
"""
)
Shape comparison:
- Original t-map image shape : (53, 63, 46)
- Resampled t-map image shape: (99, 117, 95)
- Template image shape       : (99, 117, 95)

Affine comparison:
- Original t-map image affine :
 [[  -3.    0.    0.   78.]
 [   0.    3.    0. -112.]
 [   0.    0.    3.  -50.]
 [   0.    0.    0.    1.]]
- Resampled t-map image affine:
 [[   2.    0.    0.  -98.]
 [   0.    2.    0. -134.]
 [   0.    0.    2.  -72.]
 [   0.    0.    0.    1.]]
- Template image affine       :
 [[   2.    0.    0.  -98.]
 [   0.    2.    0. -134.]
 [   0.    0.    2.  -72.]
 [   0.    0.    0.    1.]]

Finally, result images are displayed using nilearn plotting module.

from nilearn import plotting

plotting.plot_stat_map(
    stat_img,
    bg_img=template,
    cut_coords=(36, -27, 66),
    threshold=3,
    title="t-map in original resolution",
)
plotting.plot_stat_map(
    resampled_stat_img,
    bg_img=template,
    cut_coords=(36, -27, 66),
    threshold=3,
    title="Resampled t-map",
)
plotting.show()
  • plot resample to template
  • plot resample to template

Total running time of the script: (0 minutes 3.396 seconds)

Estimated memory usage: 9 MB

Gallery generated by Sphinx-Gallery