spm.Coregister() error

[AnnaZhuravleva]

Summary

I try to use nipype.iterfaces.spm.Coregister(), but I got the following error

Actual behavior

ValueError Traceback (most recent call last)
~\Desktop\fmri\lib\site-packages\nipype\utils\spm_docs.py in _strip_header(doc)
48 hdr = 'NIPYPE'
---> 49 # There's some weird cruft at the end of the docstring, almost looks like
50 # the hex for the escape character 0x1b.

ValueError: substring not found

The above exception was the direct cause of the following exception:

OSError Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_3584\2699162709.py in
----> 1 spm.Coregister()

~\Desktop\fmri\lib\site-packages\nipype\interfaces\spm\base.py in init(self, **inputs)
308 def set_mlab_paths(cls, matlab_cmd=None, paths=None, use_mcr=None):
309 cls._matlab_cmd = matlab_cmd
--> 310 cls._paths = paths
311 cls._use_mcr = use_mcr
312 info_dict = Info.getinfo(

~\Desktop\fmri\lib\site-packages\nipype\interfaces\base\core.py in init(self, from_file, resource_monitor, ignore_exception, **inputs)
196 def _check_requires(self, spec, name, value):
197 """ check if required inputs are satisfied
--> 198 """
199 if spec.requires:
200 values = [

~\Desktop\fmri\lib\site-packages\nipype\interfaces\base\core.py in _check_version_requirements(self, trait_object, permissive)
293 due.cite(**r)
294
--> 295 def run(self, cwd=None, ignore_exception=None, **inputs):
296 """Execute this interface.
297

~\Desktop\fmri\lib\site-packages\nipype\interfaces\spm\base.py in version(self)
359
360 @Property
--> 361 def jobname(self):
362 return self._jobname
363

~\Desktop\fmri\lib\site-packages\nipype\interfaces\spm\base.py in getinfo(klass, matlab_cmd, paths, use_mcr)
237 klass._path = out_dict['path']
238 klass._name = out_dict['name']
--> 239 klass._command = matlab_cmd
240 klass._paths = paths
241 return out_dict

~\Desktop\fmri\lib\site-packages\nipype\utils\spm_docs.py in _strip_header(doc)
49 # There's some weird cruft at the end of the docstring, almost looks like
50 # the hex for the escape character 0x1b.
---> 51 cruft = '\x1b'
52 try:
53 index = doc.index(hdr)

OSError: This docstring was not generated by Nipype!

Expected behavior

No errors

Script/Workflow details

import nipype.interfaces.spm as spm
coreg = spm.Coregister()

Platform details:

{'commit_hash': 'f2bbcc917',
 'commit_source': 'installation',
 'networkx_version': '2.6.3',
 'nibabel_version': '3.2.2',
 'nipype_version': '1.1.7',
 'numpy_version': '1.21.6',
 'pkg_path': 'C:\\Users\\NeuroLing\\Desktop\\fmri\\lib\\site-packages\\nipype',
 'scipy_version': '1.7.3',
 'sys_executable': 'C:\\Users\\NeuroLing\\Desktop\\fmri\\Scripts\\python.exe',
 'sys_platform': 'win32',
 'sys_version': '3.7.5 (tags/v3.7.5:5c02a39a0b, Oct 15 2019, 00:11:34) [MSC '
                'v.1916 64 bit (AMD64)]',
 'traits_version': '6.3.2'}

Execution environment

Choose one

• Container [Tag: ???]
• My python environment inside container [Base Tag: ???]
• My python environment outside container

[gr33n1]

Hi @AnnaZhuravleva, I am getting the same Error but from different way:
My code:
spm.Realign()
When this runs it uses matlab to run the follwing (base.py lines 217):

mlab.inputs.script = """
                  if isempty(which('spm')),
                  throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
                  end;
                  spm_path = spm('dir');
                  [name, version] = spm('ver');
                  fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version);
                  exit;
"""
try:
    out = mlab.run()

I run it in Matlab and got :

>> isempty(which('spm'))
        
        ans =
        
          logical
        
           0
        
>> [name, version] = spm('ver');
fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version);
      NIPYPE path:C:\Program Files\MATLAB\R2022b\toolbox\spm12\spm12|name:SPM12|release:7771

so as you can see i have result from this script, but when checking the "out" variable here (line 239):
out = sd._strip_header(out.runtime.stdout)
Stdout is "" empty string

So I think the problem is Somhow related to the answer of the script from Matlab, how to fix it ??
Thanks!

[mcsitter]

After attempting to start MATLAB, I received a message stating that the license was not up to date. After updating the license, the issue was resolved.