OSError: This docstring was not generated by Nipype!

Summary of what happened:

I am trying to use the SPM standalone tool with Python and the Matlab Common Runtime installation, but I am getting an error that the docstring returned by MCR was not generated by nipype

Command used (and if a helper script was used, a link to the helper script or the command generated):

from nipype.interfaces import spm
import os
os.environ['FORCE_SPMMCR'] = '1'

matlab_cmd = '/Users/cjohnson44/Documents/MATLAB/spm12/run_spm12.sh /Applications/MATLAB/MATLAB_Runtime/v97/ script'
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)


SPM12, Matlab Runtime R2022b

Environment (Docker, Singularity / Apptainer, custom installation):

Local conda build

Relevant log outputs (up to 20 lines):

stty: stdin isn't a terminal
ValueError                                Traceback (most recent call last)
File /opt/anaconda3/envs/matlabengine/lib/python3.10/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[7], line 3
      1 from nipype.interfaces import spm
      2 matlab_cmd = '/Users/cjohnson44/spm12_standalone/run_spm12.sh /Applications/MATLAB/MATLAB_Runtime/R2022b/ script'
----> 3 spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
      4 spm.SPMCommand().version

File /opt/anaconda3/envs/matlabengine/lib/python3.10/site-packages/nipype/interfaces/spm/base.py:322, in SPMCommand.set_mlab_paths(cls, matlab_cmd, paths, use_mcr)
    320 cls._paths = paths
    321 cls._use_mcr = use_mcr
--> 322 info_dict = Info.getinfo(matlab_cmd=matlab_cmd, paths=paths, use_mcr=use_mcr)

File /opt/anaconda3/envs/matlabengine/lib/python3.10/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 /opt/anaconda3/envs/matlabengine/lib/python3.10/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!

Dear @cjohnson44 ,

It looks like you are running this on MacOS?

Have you checked that you are using an spm12 standalone version that was compiled on Mac?

Have you checked if this is an Apple silicon system? If yes, have you tried disabling Rosetta.

In the project https://www.neurodesk.org we got SPM12 standalone to work with nipype inside a Linux system running through docker with disabled Rosetta support on apple silicon - but while experimenting with this I saw the same errors.

I hope this helps :slight_smile:
Kind regards

Hi Steffen,

Thank you for your reply! I am on MacOS Monterey (12.6.8) with an Intel i7 chip. The standalone spm12 can compile from the command line with the same command used in the matlab_cmd from my code above, so I am quite certain that it is the correctly compiled version for my system.

The problem seems to be with how Nipype handles the commands. I will keep looking into it and update the thread if I figure it out!


I went to the source of the error in the sd._strip_header() method and printed out the stdout (original code and change shown below:

        mlab = MatlabCommand(matlab_cmd=matlab_cmd, resource_monitor=False)
        mlab.inputs.mfile = False
        if paths:  
            mlab.inputs.paths = paths
        if use_mcr:
            mlab.inputs.nodesktop = Undefined
            mlab.inputs.nosplash = Undefined
            mlab.inputs.single_comp_thread = Undefined
            mlab.inputs.mfile = True
            mlab.inputs.uses_mcr = True
        mlab.inputs.script = """
if isempty(which('spm')),
throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
spm_path = spm('dir');
[name, version] = spm('ver');
fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version);
            out = mlab.run()
        except (IOError, RuntimeError) as e:
            return None
        print(out.runtime.stdout) # added line here
        out = sd._strip_header(out.runtime.stdout)

Running this with my original check method yields:

stty: stdin isn't a terminal
SPM12, version 7771 (standalone)
MATLAB, version (R2019b) Update 9
 ___  ____  __  __                                            
/ __)(  _ \(  \/  )                                           
\__ \ )___/ )    (   Statistical Parametric Mapping           
(___/(__)  (_/\/\_)  SPM12 - https://www.fil.ion.ucl.ac.uk/spm/

Executing /Users/cjohnson44/pyscript.m at 02-Jul-2024 11:20:39:
Executing /Users/cjohnson44/pyscript.m at 02-Jul-2024 11:20:39:
MATLAB Version: (R2019b) Update 9
MATLAB License Number: unknown
Operating System: macOS  Version: 12.6.8 Build: 21G725 
Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
MATLAB                                                Version 9.7         (R2019b)                
FieldTrip                                             Version unknown     www.fieldtriptoolbox.org
MATLAB Compiler                                       Version 7.1         (R2019b)                
RICOH MEG Reader toolbox for MATLAB                   Version 1.0.2                               
Statistical Parametric Mapping                        Version 7771        (SPM12)                 
Yokogawa MEG Reader toolbox for MATLAB                Version 1.5.1                               
NIPYPE path:/Users/cjohnson44/Documents/MATLAB/spm12/spm12.app/Contents/MacOS/spm12_mcr/Users/spm/spm12|name:SPM12|release:7771

stty: stdin isn't a terminal

                            < M A T L A B (R) >
                  Copyright 1984-2022 The MathWorks, Inc.
              R2022b Update 5 ( 64-bit (maci64)
                             February 10, 2023

To get started, type doc.
For product information, visit www.mathworks.com.

It appears that the nipype engine is actually spinning up both the SPM12 standalone, as well as a MATLAB engine. I was able to fix this issue by removing MATLAB from my PATH before starting my jupyter lab, and now all is running well!