Summary of what happened:
When trying to filter data using tproject.run(), get OSError: No command “3dTproject” found on host. Please check that the corresponding package is installed. I know Nipype is working, but not sure how to troubleshoot this.
Command used (and if a helper script was used, a link to the helper script or the command generated):
Code from Neuroimaging in Python - Pipelines and Interfaces — nipy pipeline and interfaces package
from nipype.interfaces import afni
tproject = afni.TProject()
tproject.inputs.in_file = ‘functional.nii’ #change file name and directory
tproject.inputs.bandpass = (0.00667, 99999)
tproject.inputs.polort = 3
tproject.inputs.automask = True
tproject.inputs.out_file = ‘projected.nii.gz’
tproject.cmdline
res = tproject.run() # doctest: +SKIP
Version:
Python 3.9.12
Environment (Docker, Singularity, custom installation):
Jupyter Notebook through Anaconda
Data formatted according to a validatable standard? Please provide the output of the validator:
BIDS
Relevant log outputs (up to 20 lines):
OSError Traceback (most recent call last)
Input In [4], in <cell line: 9>()
7 tproject.inputs.out_file = ‘projected.nii.gz’
8 tproject.cmdline
----> 9 res = tproject.run()
File ~/opt/anaconda3/lib/python3.9/site-packages/nipype/interfaces/base/core.py:398, in BaseInterface.run(self, cwd, ignore_exception, **inputs)
396 # Run interface
397 runtime = self._pre_run_hook(runtime)
→ 398 runtime = self._run_interface(runtime)
399 runtime = self._post_run_hook(runtime)
400 # Collect outputs
File ~/opt/anaconda3/lib/python3.9/site-packages/nipype/interfaces/afni/base.py:124, in AFNICommandBase._run_interface(self, runtime, correct_return_codes)
122 if platform == “darwin”:
123 runtime.environ[“DYLD_FALLBACK_LIBRARY_PATH”] = “/usr/local/afni/”
→ 124 return super(AFNICommandBase, self)._run_interface(
125 runtime, correct_return_codes
126 )
File ~/opt/anaconda3/lib/python3.9/site-packages/nipype/interfaces/base/core.py:753, in CommandLine._run_interface(self, runtime, correct_return_codes)
750 cmd_path = which(executable_name, env=runtime.environ)
752 if cmd_path is None:
→ 753 raise IOError(
754 'No command “%s” found on host %s. Please check that the ’
755 “corresponding package is installed.”
756 % (executable_name, runtime.hostname)
757 )
759 runtime.command_path = cmd_path
760 runtime.dependencies = (
761 get_dependencies(executable_name, runtime.environ)
762 if self._ldd
763 else “”
764 )
OSError: No command “3dTproject” found on host. Please check that the corresponding package is installed.