dcbc.py

[nmskhan]

Hi
Thank you for sharing the codes. I tried to run ... 01_globalconnectivity.sh script, the dcbc.py came up with an error saying deprecation error or warning with several instances.
My computer was installed python 3.9. I am not sure which version of python is compatible with the code. Could you please suggest to me how to fix that?

Error:
% test1/rsfMRI-global-local-connectivity-main/dcbc.py:9: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

• deprecated from version: 3.0

• Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  mask = mask.get_data().astype(bool)
  /Users/kh/Downloads/test1/rsfMRI-global-local-connectivity-main/dcbc.py:10: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

• deprecated from version: 3.0

• Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  imgdata = img.get_data()
  /Users/kh/Downloads/test1/rsfMRI-global-local-connectivity-main/dcbc.py:12: DeprecationWarning: get_header method is deprecated.
  Please use the img.header property instead.

• deprecated from version: 2.1

• Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  voxsize = np.array(img.get_header().get_zooms()[0:3]).reshape(1,3)
  Traceback (most recent call last):
  File "/Users/kh/Downloads/test1/rsfMRI-global-local-connectivity-main/dcbc.py", line 80, in
  main()
  File "/Users/kh/Downloads/test1/rsfMRI-global-local-connectivity-main/dcbc.py", line 75, in main
  result = dcbc(img, mask, args.radius)
  File "/Users/kh/Downloads/test1/rsfMRI-global-local-connectivity-main/dcbc.py", line 14, in dcbc
  numtps = img.get_shape()[3]
  File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/nibabel/deprecator.py", line 181, in deprecated_func
  raise error_class(message)
  nibabel.deprecator.ExpiredDeprecationError: get_shape method is deprecated.
  Please use the img.shape property instead.

• deprecated from version: 1.2

• Raises <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 3.0

[edeguzman]

@nmskhan, you need to use Python 2. We have not updated the code to be compatible with Python 3 yet.