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preprocessed-connectomes-project / quality-assessment-protocol

Scripts and documentation for the PCP's protocol for assessing data quality.
BSD 3-Clause "New" or "Revised" License
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Cannot run qap_measures_pipeline #126

Open bbiekman opened 5 years ago

bbiekman commented 5 years ago

I'm having issues with running qap_measures_pipeline.py. I get the message below, similar to what was brought up in #120 and #125:

/usr/lib/python2.7/site-packages/qap-1.0.8b-py2.7.egg/qap/script_utils.py:29: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. config = yaml.load(f) Traceback (most recent call last): File "/bin/qap_measures_pipeline.py", line 5, in pkg_resources.run_script('qap==1.0.8b', 'qap_measures_pipeline.py') File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 540, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 1455, in run_script execfile(script_filename, namespace, namespace) File "/usr/lib/python2.7/site-packages/qap-1.0.8b-py2.7.egg/EGG-INFO/scripts/qap_measures_pipeline.py", line 10, in obj.run() File "/usr/lib/python2.7/site-packages/qap-1.0.8b-py2.7.egg/qap/cli.py", line 552, in run from nipype.pipeline.plugins.callback_log import log_nodes_cb ImportError: No module named callback_log

I tried downgrading nipype to 0.13.1, as suggested by anibalsolon and subsequently got the error message below: Traceback (most recent call last): File "/home/bbiekman/.local/bin/qap_anatomical_spatial.py", line 10, in obj.run() File "/home/bbiekman/.local/lib/python2.7/site-packages/qap/cli.py", line 611, in run results.append(self.run_one_bundle(idx)) File "/home/bbiekman/.local/lib/python2.7/site-packages/qap/cli.py", line 446, in run_one_bundle rt = run_workflow(wfargs) File "/home/bbiekman/.local/lib/python2.7/site-packages/qap/cli.py", line 879, in run_workflow config, name) File "/home/bbiekman/.local/lib/python2.7/site-packages/qap/qap_workflows.py", line 407, in qap_anatomical_spatial_workflow qap_mask_workflow(workflow, resource_pool, config, name) File "/home/bbiekman/.local/lib/python2.7/site-packages/qap/qap_workflows.py", line 74, in qap_mask_workflow config, name) File "/home/bbiekman/.local/lib/python2.7/site-packages/qap/anatomical_preproc.py", line 371, in afni_anatomical_linear_registration config, name) File "/home/bbiekman/.local/lib/python2.7/site-packages/qap/anatomical_preproc.py", line 58, in anatomical_reorient_workflow anat_deoblique = pe.Node(interface=preprocess.Refit(), AttributeError: 'module' object has no attribute 'Refit'

What should I do to ensure that I can use qap?