Hi everyone~I am new to use afni.bandfilter to filter rs-fmri after using TSNR.
Here is my code:
from nipype.interfaces.afni import Bandpass
out_file=’/home/work_preproc/’
bandpass=Node(Bandpass(despike= False,highpass=0.01,lowpass=0.1,no_detrend=True,out_file=out_file),name=‘Bandfilter’)
preproc.connect([(detrend,bandpass,[(‘detrended_file’,‘in_file’)])])
I got the following error:
{‘node’: work_preproc.Bandfilter.a0.b191,
‘traceback’: [‘Traceback (most recent call last):\n’,
’ File “/home/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 482, in aggregate_outputs\n setattr(outputs, key, val)\n’,
’ File “/home/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py”, line 317, in validate\n value = super(File, self).validate(objekt, name, value, return_pathlike=True)\n’,
’ File “/home/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py”, line 141, in validate\n self.error(objekt, name, str(value))\n’,
’ File “/home/anaconda3/lib/python3.7/site-packages/traits/trait_handlers.py”, line 236, in error\n object, name, self.full_info(object, name, value), value\n’,
“traits.trait_errors.TraitError: The ‘out_file’ trait of an AFNICommandOutputSpec instance must be a pathlike object or string representing an existing file, but a value of ‘/home/research/beijing_out/bandfilter+orig.BRIK’ <class ‘str’> was specified.\n”,
‘\nDuring handling of the above exception, another exception occurred:\n\n’,
‘Traceback (most recent call last):\n’,
’ File “/home/anaconda3/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node\n result[‘result’] = node.run(updatehash=updatehash)\n’,
’ File “/home/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 479, in run\n result = self._run_interface(execute=True)\n’,
’ File “/home/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 585, in _run_interface\n return self._run_command(execute)\n’,
’ File “/home/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 678, in _run_command\n result = self._interface.run(cwd=outdir)\n’,
’ File “/home/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 384, in run\n outputs = self.aggregate_outputs(runtime)\n’,
’ File “/home/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 487, in aggregate_outputs\n raise FileNotFoundError(msg)\n’,
“FileNotFoundError: No such file or directory ‘/home/research/bandfilter+orig.BRIK’ for output ‘out_file’ of a Bandpass interface\n”]}
It seems that I got wrong out_file, but I really do not know how to fix it. Thanks for any help~