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

[Ian Malone]

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