nipype
nipype copied to clipboard
Published
20 hours ago •
nipy
nipy
Issue running nipype.interfaces.spm
trafficstars
Hi, I am experiencing issues running nipype.interfaces.spm in my windows machine. I get "This docstring was not generated by Nipype! " error message when I run the following command. Any assistance to resolve this issue would be appreciated. Thank you!
Actual behavior
>>import nipype.interfaces.spm as spm^M
>>est = spm.EstimateContrast()
'stty' is not recognized as an internal or external command,
operable program or batch file.
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
File ~\anaconda3\envs\test\lib\site-packages\nipype\utils\spm_docs.py:49, in _strip_header(doc)
48 try:
---> 49 index = doc.index(hdr)
50 except ValueError as e:
ValueError: substring not found
The above exception was the direct cause of the following exception:
OSError Traceback (most recent call last)
Cell In[11], line 2
1 import nipype.interfaces.spm as spm
----> 2 est = spm.EstimateContrast()
File ~\anaconda3\envs\test\lib\site-packages\nipype\interfaces\spm\base.py:309, in SPMCommand.__init__(self, **inputs)
308 def __init__(self, **inputs):
--> 309 super(SPMCommand, self).__init__(**inputs)
310 self.inputs.on_trait_change(
311 self._matlab_cmd_update, ["matlab_cmd", "mfile", "paths", "use_mcr"]
312 )
313 self._find_mlab_cmd_defaults()
File ~\anaconda3\envs\test\lib\site-packages\nipype\interfaces\base\core.py:197, in BaseInterface.__init__(self, from_file, resource_monitor, ignore_exception, **inputs)
194 # Create input spec, disable any defaults that are unavailable due to
195 # version, and then apply the inputs that were passed.
196 self.inputs = self.input_spec()
--> 197 unavailable_traits = self._check_version_requirements(
198 self.inputs, permissive=True
199 )
200 if unavailable_traits:
201 self.inputs.trait_set(**{k: Undefined for k in unavailable_traits})
File ~\anaconda3\envs\test\lib\site-packages\nipype\interfaces\base\core.py:295, in BaseInterface._check_version_requirements(self, trait_object, permissive)
292 check = dict(min_ver=lambda t: t is not None)
293 names = trait_object.trait_names(**check)
--> 295 if names and self.version:
296 version = LooseVersion(str(self.version))
297 for name in names:
File ~\anaconda3\envs\test\lib\site-packages\nipype\interfaces\spm\base.py:357, in SPMCommand.version(self)
355 @property
356 def version(self):
--> 357 info_dict = Info.getinfo(
358 matlab_cmd=self.inputs.matlab_cmd,
359 paths=self.inputs.paths,
360 use_mcr=self.inputs.use_mcr,
361 )
362 if info_dict:
363 return "%s.%s" % (info_dict["name"].split("SPM")[-1], info_dict["release"])
File ~\anaconda3\envs\test\lib\site-packages\nipype\interfaces\spm\base.py:238, in Info.getinfo(klass, matlab_cmd, paths, use_mcr)
235 klass._paths = paths
236 return None
--> 238 out = sd._strip_header(out.runtime.stdout)
239 out_dict = {}
240 for part in out.split("|"):
File ~\anaconda3\envs\test\lib\site-packages\nipype\utils\spm_docs.py:51, in _strip_header(doc)
49 index = doc.index(hdr)
50 except ValueError as e:
---> 51 raise IOError("This docstring was not generated by Nipype!\n") from e
53 index += len(hdr)
54 index += 1
OSError: This docstring was not generated by Nipype!
Execution environment
python version 3.9.16 nipype version 1.8.4
Nipype is not supported on Windows. You may be able to use the Windows Subsystem for Linux to get it working, however. I don't know, though.
Hi @effigies, I am having a similar issue and is unrelated to the OS used since I am running it in Linux.
Loading SPM Interface using nipype release 1.6,
In [1]: import nipype; nipype.__version__
Out[1]: '1.6.1'
In [2]: import nipype.interfaces.spm as spm
240610-16:54:36,61 nipype.utils WARNING:
A newer version (1.8.4) of nipy/nipype is available. You are using 1.6.1
In [3]: spm.SPMCommand.set_mlab_paths(matlab_cmd='spm12 script', use_mcr=True)
In [4]: spm.Realign()
Out[4]: <nipype.interfaces.spm.preprocess.Realign at 0x7f1f84c03908>
Loading SPM Interface using nipype release 1.7 or above,
In [1]: import nipype; nipype.__version__
Out[1]: '1.8.6'
In [2]: import nipype.interfaces.spm as spm
In [3]: spm.SPMCommand.set_mlab_paths(matlab_cmd='spm12 script', use_mcr=True)
In [4]: spm.Realign()
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/tmp/p3/lib/python3.7/site-packages/nipype/utils/spm_docs.py in _strip_header(doc)
48 try:
---> 49 index = doc.index(hdr)
50 except ValueError as e:
ValueError: substring not found
The above exception was the direct cause of the following exception:
OSError Traceback (most recent call last)
<ipython-input-3-9ebc2828a699> in <module>
----> 1 spm.Realign()
/tmp/p3/lib/python3.7/site-packages/nipype/interfaces/spm/base.py in __init__(self, **inputs)
307
308 def __init__(self, **inputs):
--> 309 super(SPMCommand, self).__init__(**inputs)
310 self.inputs.on_trait_change(
311 self._matlab_cmd_update, ["matlab_cmd", "mfile", "paths", "use_mcr"]
/tmp/p3/lib/python3.7/site-packages/nipype/interfaces/base/core.py in __init__(self, from_file, resource_monitor, ignore_exception, **inputs)
196 self.inputs = self.input_spec()
197 unavailable_traits = self._check_version_requirements(
--> 198 self.inputs, permissive=True
199 )
200 if unavailable_traits:
/tmp/p3/lib/python3.7/site-packages/nipype/interfaces/base/core.py in _check_version_requirements(self, trait_object, permissive)
293 names = trait_object.trait_names(**check)
294
--> 295 if names and self.version:
296 version = LooseVersion(str(self.version))
297 for name in names:
/tmp/p3/lib/python3.7/site-packages/nipype/interfaces/spm/base.py in version(self)
358 matlab_cmd=self.inputs.matlab_cmd,
359 paths=self.inputs.paths,
--> 360 use_mcr=self.inputs.use_mcr,
361 )
362 if info_dict:
/tmp/p3/lib/python3.7/site-packages/nipype/interfaces/spm/base.py in getinfo(klass, matlab_cmd, paths, use_mcr)
236 return None
237
--> 238 out = sd._strip_header(out.runtime.stdout)
239 out_dict = {}
240 for part in out.split("|"):
/tmp/p3/lib/python3.7/site-packages/nipype/utils/spm_docs.py in _strip_header(doc)
49 index = doc.index(hdr)
50 except ValueError as e:
---> 51 raise IOError("This docstring was not generated by Nipype!\n") from e
52
53 index += len(hdr)
OSError: This docstring was not generated by Nipype!
Any ideas of what's going on?
No. If you're using IPython, you can set the %pdb magic, and then move up and down the trace to see what the values are.
For example, in getinfo(), what is the value of out.runtime.stdout?
Well, that's embarrassing but it works fine now, no matter what I try but I am unable to reproduce it:
(venv_p3) jordi@dev-barcelonabrainimaging:~> ipython
Python 3.7.2 (default, Mar 26 2019, 12:41:22)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.20.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: import nipype.interfaces.spm as spm
In [2]: import nipype; nipype.__version__
Out[2]: '1.8.6'
In [3]: spm.SPMCommand.set_mlab_paths(matlab_cmd='spm12 script', use_mcr=True)
In [4]: spm.Realign()
Out[4]: <nipype.interfaces.spm.preprocess.Realign at 0x7f55ca6aaa58>
Forget it then. Thanks for your prompt reply!