[Neuroimaging] Plotting a Single ROI from an Atlas

[Gael Varoquaux]

Hi Lou,

Here is code that I believe does what you want, with a bit of comments to
explain briefly how it works. I suggest that you study each step to
understand what it does.

"""
from nilearn import datasets, image, plotting

# Retrieve the AAL atlas
aal_atlas = datasets.fetch_atlas_aal('SPM12')

# Now find the position of the Rectus_R in the list of region
# labels, and use the corresponding list of indices of the image to
# convert it to the index value in the map
rectus_r_idx = aal_atlas.indices[aal_atlas.labels.index('Rectus_R')]

# Select only the voxels of the map for which the value is equal to the
# this index.
rectus_r_map = image.math_img('img == %s' % rectus_r_idx,
                              img=aal_atlas.maps)

# The resulting map is a binay map that contains only the Rectus_R, we
# can plot it.
plotting.plot_roi(rectus_r_map, title='Rectus_R')
"""

Best,

Gaël

On Thu, Jan 04, 2018 at 03:09:12PM -0800, Lodewijk Brand wrote:
> Hi All,

> I am trying to figure out a way to plot specific ROIs from an atlas in Python.
> I am looking specifically at the AAL atlas:

> aal_atlas = datasets.fetch_atlas_aal('SPM12')


> I would like to plot individual regions (eg. 'Rectus_R', 'Insula_L',
> 'Insula_R', etc.) that are specified within the atlas. I've been able to plot
> the entire brain image with all the ROIs at once cannot seem to figure out how
> to do each one individually. Any help/direction would be greatly appreciated! 

> Best,

> Lou

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-- 
    Gael Varoquaux
    Senior Researcher, INRIA Parietal
    NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France
    Phone:  ++ 33-1-69-08-79-68
    http://gael-varoquaux.info            http://twitter.com/GaelVaroquaux