Visualizing Neuroimaging Volume Files

This is to write a function that I want to later turn into a package. Here are some of the things I want this to do (not necessarily:

Show a fslview like representation of the volume with a given coordinate
Make a niak_montage like montage of the volume that covers the whole brain.
Have some summary metrics of the volume

Pierre generates one big matrix with all the images together and then just visualizes this. I think this is a pretty good template for what I want to do as well.



In [54]:

    
# Imports
import os
import numpy as np
import nibabel as nib
from scipy import ndimage as sn
from matplotlib import pyplot as plt



In [6]:

    
# Paths
in_file = '/home/surchs/Test/mni_152.nii.gz'



In [89]:

    
# Load the file and pick a volume
data = nib.load(in_file).get_data()
rolled = sn.interpolation.rotate(data, 0, [1,2])
print('The input file has the dimension {}'.format(data.shape))
slic_x = rolled[100,:,:]
slic_y = rolled[:,120,:]
slic_z = rolled[:,:,120]
print('The test slice has the dimension {}'.format(slic.shape))









    



The input file has the dimension (197, 233, 189)
The test slice has the dimension (197, 189)



In [90]:

    
f = plt.figure()
ax_x = f.add_subplot(131)
ax_x.imshow(slic_x, interpolation='nearest')
ax_y = f.add_subplot(132)
ax_y.imshow(slic_y, interpolation='nearest')
ax_z = f.add_subplot(133)
ax_z.imshow(slic_z, interpolation='nearest')









    Out[90]:





<matplotlib.image.AxesImage at 0x7ffa5388f750>



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