Welcome to the AFQ-Browser exploratory notebook

What is this thing?

This is a Jupyter notebook. You can add code cells to this notebook, and execute Python code that you write in these cells, by pressing the shift and enter keys on your keyboard.

For example:



In [1]:

    
a = 1
print(a)

To embed figures in the notebook, please use the following Jupyter command at the top of your notebook:



In [2]:

    
%matplotlib inline

Reading AFQ-browser data

To read data in from the AFQ-browser, you can use the Pandas library.



In [3]:

    
import pandas as pd



In [4]:

    
subjects = pd.read_csv('./data/subjects.csv')



In [5]:

    
subjects.head()



In [6]:

    
nodes = pd.read_csv('./data/nodes.csv')



In [7]:

    
nodes.head()









    Out[7]:







  
    
      
      subjectID
      tractID
      nodeID
      rd
      md
      cl
      torsion
      curvature
      fa
      ad
      volume
    
  
  
    
      0
      patient_01
      Left Thalamic Radiation
      0
      0.613340
      0.851832
      0.257362
      -0.065856
      0.137844
      0.452992
      1.328816
      70.0
    
    
      1
      patient_01
      Left Thalamic Radiation
      1
      0.611204
      0.848955
      0.256652
      -0.087893
      0.153220
      0.453549
      1.324456
      60.0
    
    
      2
      patient_01
      Left Thalamic Radiation
      2
      0.608178
      0.843154
      0.254787
      -0.244466
      0.092622
      0.452349
      1.313105
      76.0
    
    
      3
      patient_01
      Left Thalamic Radiation
      3
      0.604815
      0.837168
      0.253062
      -0.533194
      0.027443
      0.451471
      1.301873
      55.0
    
    
      4
      patient_01
      Left Thalamic Radiation
      4
      0.601006
      0.831444
      0.251759
      0.272117
      0.047876
      0.451726
      1.292319
      71.0

For an example analysis, see our example analysis notebook



In [ ]:

	Unnamed: 0	patient	score	session	subjectID
0	0	1	0.194764	1	patient_01
1	1	1	0.225922	1	patient_02
2	2	1	0.170708	1	patient_03
3	3	0	0.227664	1	control_01
4	4	0	0.435699	1	control_02

	subjectID	tractID	nodeID	rd	md	cl	torsion	curvature	fa	ad	volume
0	patient_01	Left Thalamic Radiation	0	0.613340	0.851832	0.257362	-0.065856	0.137844	0.452992	1.328816	70.0
1	patient_01	Left Thalamic Radiation	1	0.611204	0.848955	0.256652	-0.087893	0.153220	0.453549	1.324456	60.0
2	patient_01	Left Thalamic Radiation	2	0.608178	0.843154	0.254787	-0.244466	0.092622	0.452349	1.313105	76.0
3	patient_01	Left Thalamic Radiation	3	0.604815	0.837168	0.253062	-0.533194	0.027443	0.451471	1.301873	55.0
4	patient_01	Left Thalamic Radiation	4	0.601006	0.831444	0.251759	0.272117	0.047876	0.451726	1.292319	71.0