t1 volume processing raise errors
Sidong Zhang
clinica run t1-volume-tissue-segmentation BIDS_DIR CAPS_DIR
Traceback (most recent call last):
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/nipype/utils/spm_docs.py", line 49, in _strip_header
index = doc.index(hdr)
ValueError: substring not found
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/sidongzhang/miniconda3/envs/clinica_dev/bin/clinica", line 5, in <module>
main()
File "/mnt/nfs/work1/mfiterau/ADNI_TADPOLE/clinica/clinica/cmdline.py", line 89, in main
cli()
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/click/core.py", line 1128, in __call__
return self.main(*args, **kwargs)
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/mnt/nfs/work1/mfiterau/ADNI_TADPOLE/clinica/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py", line
68, in cli
else pipeline.run()
File "/mnt/nfs/work1/mfiterau/ADNI_TADPOLE/clinica/clinica/pipelines/engine.py", line 261, in run
self.build()
File "/mnt/nfs/work1/mfiterau/ADNI_TADPOLE/clinica/clinica/pipelines/engine.py", line 25, in func_wrapper
res = func(self, *args, **kwargs)
File "/mnt/nfs/work1/mfiterau/ADNI_TADPOLE/clinica/clinica/pipelines/engine.py", line 232, in build
self.build_core_nodes()
File "/mnt/nfs/work1/mfiterau/ADNI_TADPOLE/clinica/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_pipeline.py",
line 163, in build_core_nodes
new_segment = npe.Node(spm.NewSegment(), name="2-SpmSegmentation")
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/nipype/interfaces/spm/preprocess.py", line 1869, in __init__
_local_version = SPMCommand().version
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/nipype/interfaces/spm/base.py", line 310, in __init__
super(SPMCommand, self).__init__(**inputs)
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 197, in __init__
unavailable_traits = self._check_version_requirements(
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 295, in _check_version_re
quirements
if names and self.version:
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/nipype/interfaces/spm/base.py", line 358, in version
info_dict = Info.getinfo(
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/nipype/interfaces/spm/base.py", line 239, in getinfo
out = sd._strip_header(out.runtime.stdout)
File "/home/sidongzhang/miniconda3/envs/clinica_dev/lib/python3.8/site-packages/nipype/utils/spm_docs.py", line 51, in _strip_header
raise IOError("This docstring was not generated by Nipype!\n") from e
OSError: This docstring was not generated by Nipype!
