[Neuroimaging] nipype node, execution and original inputs difference?

[Satrajit Ghosh]

hi ian,

that's very surprising. one scenario would be if this node was set as a
MapNode, but it doesn't look like it.

a way to debug this would be to:

import os
from nipype.utils.filemanip import loadpkl

node_wd = '/path/to/node/wd'
node = loadpkl(os.path.join(node_wd, '_node.pklz')
print(node.inputs)
node.base_dir = '/somepath' # otherwise it will overwrite node_wd
result = node.run()

there is also an _inputs.pklz in node_wd which shows the inputs to the node.

feel free to open an issue on github where this can be tracked.

cheers,

satra

On Tue, Dec 12, 2017 at 6:28 AM, Ian Malone <ibmalone at gmail.com> wrote:

> Hi,
>
> I'm trying to debug a nipype problem with the inputs to a function
> node and wondered if anyone could help.
>
> The function is meant to merge two diffusion datasets together, so
> takes lists of b vector and value files and the images themselves. If
> there's only one set of inputs it just passes them through. So far so
> good. Under every circumstance up to now it's worked as expected, but
> I've run in a case where with two inputs it behaves as if there's only
> one set.
>
> The report.rst file for the node tells me that's exactly what's happening:
>
> Original Inputs
> ---------------
> <snip>
> * in_bvals : ['/var/drc/research/tess/dtipipeline/01-0335-08-03-MR00/
> ep2ddiffFREE681p2FAD25mmiABCD.bval',
> '/var/drc/research/tess/dtipipeline/01-0335-08-03-MR00/
> ep2ddiffFREE681p2FAD25mmi.bval']
> * in_bvecs : ['/var/drc/research/tess/dtipipeline/01-0335-08-03-MR00/
> ep2ddiffFREE681p2FAD25mmiABCD.bvec',
> '/var/drc/research/tess/dtipipeline/01-0335-08-03-MR00/
> ep2ddiffFREE681p2FAD25mmi.bvec']
> * in_dwis : ['/var/drc/research/tess/dtipipeline/01-0335-08-03-MR00/
> ep2ddiffFREE681p2FAD25mmiABCD.nii.gz',
> '/var/drc/research/tess/dtipipeline/01-0335-08-03-MR00/
> ep2ddiffFREE681p2FAD25mmi.nii.gz']
>
>
> Execution Inputs
> ----------------
> <snip>
> * in_bvals : ['/var/drc/research/tess/dtipipeline/01-0335-08-03-MR00/
> ep2ddiffFREE681p2FAD25mmi.bval']
> * in_bvecs : ['/var/drc/research/tess/dtipipeline/01-0335-08-03-MR00/
> ep2ddiffFREE681p2FAD25mmi.bvec']
> * in_dwis : ['/var/drc/research/tess/dtipipeline/01-0335-08-03-MR00/
> ep2ddiffFREE681p2FAD25mmi.nii.gz']
>
>
> It appears the node inputs are set correctly, but are getting stripped
> or truncated before execution. The same pipeline behaving normally
> doesn't do this:
>
>
> Original Inputs
> ---------------
> <snip>
> * in_bvals : ['/var/lib/midas/data/lha1946/images/nii/original/3033.bval',
> '/var/lib/midas/data/lha1946/images/nii/original/3024.bval']
> * in_bvecs : ['/var/lib/midas/data/lha1946/images/nii/original/3033.bvec',
> '/var/lib/midas/data/lha1946/images/nii/original/3024.bvec']
> * in_dwis : ['/var/lib/midas/data/lha1946/images/nii/original/3033.nii.
> gz',
> '/var/lib/midas/data/lha1946/images/nii/original/3024.nii.gz']
>
>
> Execution Inputs
> ----------------
> <snip>
> * in_bvals : ['/var/lib/midas/data/lha1946/images/nii/original/3033.bval',
> '/var/lib/midas/data/lha1946/images/nii/original/3024.bval']
> * in_bvecs : ['/var/lib/midas/data/lha1946/images/nii/original/3033.bvec',
> '/var/lib/midas/data/lha1946/images/nii/original/3024.bvec']
> * in_dwis : ['/var/lib/midas/data/lha1946/images/nii/original/3033.nii.
> gz',
> '/var/lib/midas/data/lha1946/images/nii/original/3024.nii.gz']
>
>
> I don't know what can cause the execution inputs to differ from the
> initial inputs. The node and its input connections are just defined
> like this:
>
> merge_initial_dwis = pe.Node(interface=niu.Function(
>     input_names=['in_dwis', 'in_bvals', 'in_bvecs'],
>     output_names=['out_dwis', 'out_bvals', 'out_bvecs', 'out_orig_file',
>                   'out_orig_ind'],
>     function=merge_dwi_function), name='merge_initial_dwis')
>
> merge_initial_dwis.inputs.in_dwis = [os.path.abspath(f) for f in
> args.dwis]
> merge_initial_dwis.inputs.in_bvals = [os.path.abspath(f) for f in
> args.bvals]
> merge_initial_dwis.inputs.in_bvecs = [os.path.abspath(f) for f in
> args.bvecs]
>
> Any suggestions how I could try to find the cause?
>
>
> --
> imalone
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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