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nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
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Crash w/ "The behaviour of affine_transform with a one-dimensional "? #123

Closed jlhanson5 closed 7 years ago

jlhanson5 commented 7 years ago

I was just test-driving mindboggle and ran into some errors w/ how the affine transforms were being read (I think). I've included 2 crash.plz files (as a zip here; crash_archive.zip)

The first major error I'm seeing is " Executing node Convert_MRI_to_nifti_format in dir: /home/jamielh/Volumes/Hanson/Duke_PAC/proc/140313_18263/anat/Combined_mindboggle/working/20140313_18263/Mindboggle/Convert_MRI_to_nifti_format /usr/local/bin/miniconda3/lib/python3.6/site-packages/scipy/ndimage/interpolation.py:462: UserWarning: The behaviour of affine_transform with a one-dimensional array supplied for the matrix parameter has changed in scipy 0.18.0. "The behaviour of affine_transform with a one-dimensional "

Any one run into similar issues? Any info is greatly appreciated! Thanks much!

jlhanson5 commented 7 years ago

(bump) ... any thoughts?

binarybottle commented 7 years ago

That is a warning, and shouldn't be causing your crash. Instead, you seem to be missing a dependency. Both of your crash files say "The 'configparser' distribution was not found and is required by nipype". Please see the nipype issue: https://github.com/nipy/nipype/issues/1699

jlhanson5 commented 7 years ago

Ah perfect! I think pip-ing configparser & nipype[all] fixed things. Thanks much!

binarybottle commented 7 years ago

You're welcome. All the best! I'll close this issue.