search

pnlbwh / pnlNipype

PNL pipeline for NIFTI images
Other
10 stars 15 forks source link

cannot import name 'UKFTractography' from 'plumbum.cmd' #41

Closed njhunsak closed 4 years ago

njhunsak commented 4 years ago

Unable to run the ukf command:

(base)  $ ~/build/pnlNipype/exec/ukf --help
Traceback (most recent call last):
  File "/fslhome/intj5/build/pnlNipype/exec/ukf", line 6, in <module>
    from plumbum.cmd import UKFTractography
ImportError: cannot import name 'UKFTractography' from 'plumbum.cmd' (unknown location)
(base)  $

Not sure if UKFTractography needs to be one of these directories installed as part of your pipeline:

(base) $ ls -1 ~/apps/pnlbwh/pnlNipype/ 
ANTs
ANTs-build
dcm2niix
tract_querier-2019-05-08
tract_querier-d4a88aa
trainingDataT1AHCC-8141805
trainingDataT2Masks-12a14d9
ukftractography
UKFTractography-2019-05-01
UKFTractography-662c16f
UKFTractography-build
tashrifbillah commented 4 years ago

The instruction has been part of our NRRD pipeline. It looks like we missed it in our new NIFTI pipeline.

For now, you should do:

source UKFTractography-662c16f/env.sh

In the meantime, we shall include this instruction in our documentation.

njhunsak commented 4 years ago

I've confirmed that this works.