Reading AFNI BRIK & HEAD files in Python.

Here is a description of the header contents: https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.attributes.html

In Matlab you can read BRIK files using this function: https://github.com/PrincetonUniversity/princeton-mvpa-toolbox/blob/master/afni_matlab/BrikLoad.m



In [1]:

    
%pylab inline









    



Populating the interactive namespace from numpy and matplotlib



In [2]:

    
import afni



In [3]:

    
fname = "TT_N27+tlrc" # make sure you have downloaded (and g-unzipped it)
hdr,dat = afni.read(fname)



In [4]:

    
dat.shape









    Out[4]:





(161, 191, 151, 1)



In [5]:

    
f, axarr = plt.subplots(1, 3, figsize=(12,5.5))
axarr[0].imshow(dat[50,:,:,0].T,origin='lower',cmap='gray')
axarr[0].set_title("x=50")
axarr[1].imshow(dat[:,50,:,0].T,origin='lower',cmap='gray')
axarr[1].set_title("y=50")
axarr[2].imshow(dat[:,:,50,0].T,origin='lower',cmap='gray')
axarr[2].set_title("z=50")









    Out[5]:





<matplotlib.text.Text at 0x7ff8a7fa2128>

Show one slice from an EPI image.



In [6]:

    
#header["BRICK_TYPES"]
fname = "pb05.s04.pre.r01.blur+tlrc"
hdr,dat = afni.read(fname)



In [7]:

    
f, axarr = plt.subplots(1, 3, figsize=(12,5.5))
tr = 10
axarr[0].imshow(dat[50,:,:,tr].T,origin='lower')
axarr[0].set_title("x=50")
axarr[1].imshow(dat[:,50,:,tr].T,origin='lower')
axarr[1].set_title("y=50")
axarr[2].imshow(dat[:,:,50,tr].T,origin='lower')
axarr[2].set_title("z=50")









    Out[7]:





<matplotlib.text.Text at 0x7ff8a7e837b8>

Plot a time series of one voxel.



In [8]:

    
ts = dat[50,50,50,:]
plot(ts)
xlabel("EPI Volume")
ylabel("Signal")









    Out[8]:





<matplotlib.text.Text at 0x7ff8a7e1c048>



In [9]:

    
from __future__ import print_function
from ipywidgets import interact, interactive, fixed, interact_manual
import ipywidgets as widgets



In [10]:

    
def plotslices(x,y,z,t):
    
    f, axarr = plt.subplots(1, 3, figsize=(15,6.5))

    axarr[0].imshow(dat[x,:,:,t].T,origin='lower')
    axarr[0].set_title("x=%i"%x)
    axarr[1].imshow(dat[:,y,:,t].T,origin='lower')
    axarr[1].set_title("y=%i"%y)
    axarr[2].imshow(dat[:,:,z,t].T,origin='lower')
    axarr[2].set_title("z=%i"%z)


interact_manual(plotslices, 
                x=widgets.IntSlider(min=0,max=dat.shape[0]-1,step=1,value=50),
                y=widgets.IntSlider(min=0,max=dat.shape[1]-1,step=1,value=50),
                z=widgets.IntSlider(min=0,max=dat.shape[2]-1,step=1,value=50),
                t=widgets.IntSlider(min=0,max=dat.shape[3]-1,step=1,value=0));









    



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