satra
commented
11 years ago what happens if you use xfm instead of VolumeLabelFlow? this seems related to the same kind of issue you had with the graph generation. i'll try to take a look at it sometime later tonight. i have to setup a little workflow test set for this and the graph generation.
I have added antsRegistration to the pipeline, but am having trouble with antsApplyTransforms:
https://github.com/binarybottle/mindboggle/blob/master/mindboggle/mindboggler.py#L1767
The crash file ends with:
Node inputs:
args =
default_value = 0.0
dimension = 3
environ = {}
ignore_exception = False
input_image =
input_image_type =
interpolation = NearestNeighbor
invert_transform_flags =
num_threads = -1
output_image = labels.nii.gz
print_out_composite_warp_file =
reference_image =
terminal_output = stream
transforms =
Traceback: Traceback (most recent call last): File "/Users/arno/anaconda/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 349, in _send_procs_to_workers jobid].hash_exists() File "/Users/arno/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1210, in hash_exists hashed_inputs, hashvalue = self._get_hashval() File "/Users/arno/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1345, in _get_hashval self._get_inputs() File "/Users/arno/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1405, in _get_inputs self.set_input(key, deepcopy(output_value)) File "/Users/arno/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1189, in set_input setattr(self.inputs, parameter, deepcopy(val)) File "/Users/arno/anaconda/lib/python2.7/site-packages/nipype/interfaces/traits_extension.py", line 74, in validate validated_value = super( BaseFile, self ).validate( object, name, value ) File "/Users/arno/anaconda/lib/python2.7/site-packages/traits/trait_types.py", line 320, in validate self.error( object, name, value ) File "/Users/arno/anaconda/lib/python2.7/site-packages/traits/trait_handlers.py", line 170, in error value ) TraitError: The 'input_image' trait of an ApplyTransformsInputSpec instance must be an existing file name, but a value of None <type 'NoneType'> was specified. Error setting node input: Node: antsApplyTransform input: input_image results_file: /Users/arno/mindboggle_cache/workspace/Mindboggle/Volume_labels/_atlas_OASIS-TRT-20_DKT31_CMA_jointfusion_labels_in_MNI152.nii.gz/Retrieve_volume_atlas/result_Retrieve_volume_atlas.pklz value: None