[NiPype] Setting path for ants interface..

[David Gutman]

Not sure why this is being flaky, as I could have sworn this pipeline was working a couple of weeks ago last time I ran it..

IOError: N4BiasFieldCorrection could not be found on host node15

 which N4BiasFieldCorrection 

/usr/lib/ants/N4BiasFieldCorrection

It definitely exists-- but I am guessing maybe the ants module doesn't know where to look?  How do I specify the location/search path for a given underlyinh module...

Actually same question would potentially apply for FSL... if I wanted to point to the fsl4.1 vs fsl4.1.4 or whatever.. does it do it based on my current path setup or is there a way to override it... (which I am guessing there is).

dg

Node inputs:

args = <undefined>

bspline_fitting_distance = 300.0

convergence_threshold = 1e-06

dimension = 3

environ = {'ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS': '1'}

ignore_exception = False

input_image = <undefined>

n_iterations = [50, 50, 30, 20]

num_threads = 1

output_image = <undefined>

shrink_factor = 3

Traceback: 

Traceback (most recent call last):

  File "/usr/local/lib/python2.6/dist-packages/nipype/pipeline/plugins/multiproc.py", line 15, in run_node

    result['result'] = node.run(updatehash=updatehash)

  File "/usr/local/lib/python2.6/dist-packages/nipype/pipeline/engine.py", line 1128, in run

    self._run_interface()

  File "/usr/local/lib/python2.6/dist-packages/nipype/pipeline/engine.py", line 1226, in _run_interface

    self._result = self._run_command(execute)

  File "/usr/local/lib/python2.6/dist-packages/nipype/pipeline/engine.py", line 1350, in _run_command

    result = self._interface.run()

  File "/usr/local/lib/python2.6/dist-packages/nipype/interfaces/base.py", line 820, in run

    runtime = self._run_interface(runtime)

  File "/usr/local/lib/python2.6/dist-packages/nipype/interfaces/base.py", line 1097, in _run_interface

    runtime.hostname))

IOError: N4BiasFieldCorrection could not be found on host node15

--
David A Gutman, M.D. Ph.D.
Assistant Professor of Biomedical Informatics
Senior Research Scientist, Center for Comprehensive Informatics
Emory University School of Medicine

[Chris Filo Gorgolewski]

Is the PATH variable correct (i.e. includes /usr/lib/ants/) in the
_report/report.rst? Did you try running this locally?

Best,
Chris

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[David Gutman]

ill check now--- I am guessing it's a path problem... I just wasn't sure which file to look in/where to check... as it's run in the past...

so if i simply type bash command.txt it runs... but it doesn't look like the path is being sent to the module...

how / where is the global ANTS path explicitly set?

data/dgutman/GBM_WORKING_DATA/mayo_collab_gbm_reg_wf/_subject_id_TCGA-06-0129/n4bias_node_t2flair$ less 

_report/report.rst 

Node: n4bias_node_t2flair (ants)

================================

 Hierarchy : mayo_collab_gbm_reg_wf.n4bias_node_t2flair

 Exec ID : n4bias_node_t2flair.a09

Original Inputs

---------------

* args : <undefined>

* bspline_fitting_distance : 300.0

* convergence_threshold : 1e-06

* dimension : 3

* environ : {'ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS': '1'}

* ignore_exception : False

* input_image : /data/dgutman/GBM_WORKING_DATA/ASHLEE/BACKGROUNDS/TCGA-06-0129_AXIAL-T2-FLAIR_TARUN-FLAIR-ENV_BACKGROUND.nii.gz

* n_iterations : [50, 50, 30, 20]

* num_threads : 1

* output_image : <undefined>

* shrink_factor : 3

_report/report.rst (END) 

--

[Chris Filo Gorgolewski]

there is not global ants path. Just make sure that in whatever bash
session you are using to run nipype script a full path to ants
binaries is in the $PATH variable. You can check that using echo
$PATH. Set it by executing "export
PATH=/path/to/my/ants/binaries:$PATH". I recommend adding it to your
.bashrc. Alternatively you can update the PATH variable inside your
nipype script using os.environ dictionary.

Best,
Chris

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[David Gutman]

ok thanks Chris-- appreciate your feedback.

yeah I think I was running it form a "screen" and the path was funky...

thanks again