(resolved) ValueError “substring not found” when running t1-volume pipeline

[AudreyDuran]

Hi,

I am trying to run t1-volume pipeline with SPM12 standalone and clinica v0.7.2, on a custom dataset.

Here are some environment variables values defined in my ~/.bashrc:

SPM_HOME="/opt/spm12"
SPM_VERSION=12
SPM_REVISION=r7771
MATLAB_VERSION=R2019b
MCR_VERSION=v97
MCR_UPDATE=9
MCR_INHIBIT_CTF_LOCK=1
MATLABCMD="${SPM_HOME}/run_spm12.sh /opt/mcr/${MCR_VERSION} script"

When I run the pipeline, I get the following output:

2022-11-28 10:17:48,336:INFO:The t1-volume pipeline is divided into 4 parts:
        t1-volume-tissue-segmentation pipeline: Tissue segmentation, bias correction and spatial normalization to MNI space
        t1-volume-create-dartel pipeline: Inter-subject registration with the creation of a new DARTEL template
        t1-volume-dartel2mni pipeline: DARTEL template to MNI
        t1-volume-parcellation pipeline: Atlas statistics
2022-11-28 10:17:55,639:INFO:Part 1/4: Running t1-volume-segmentation pipeline.




2022-11-28 10:25:57,830:INFO:The pipeline will be run on the following 1282 image(s):
2022-11-28 10:25:57,830:INFO:   sub-00098E7F | ses-w96, ses-w0,
2022-11-28 10:25:57,830:INFO:   sub-00331D3D | ses-w0, ses-w96,
2022-11-28 10:25:57,830:INFO:   sub-003D930B | ses-w0, ses-w96,
2022-11-28 10:25:57,830:INFO:   sub-00438273 | ses-w96, ses-w0,
2022-11-28 10:25:57,830:INFO:   sub-006ACF86 | ses-w96, ses-w0,
2022-11-28 10:25:57,830:INFO:   sub-0095A525 | ses-w0, ses-w96,
2022-11-28 10:25:57,830:INFO:   sub-00DBEADC | ses-w0, ses-w96,
2022-11-28 10:25:57,830:INFO:   sub-01BA0A03 | ses-w96, ses-w0,
2022-11-28 10:25:57,830:INFO:   sub-01D4AE69 | ses-w0, ses-w96,
2022-11-28 10:25:57,830:INFO:   sub-0271F164 | ses-w0, ses-w96,
2022-11-28 10:25:57,830:INFO:   sub-02D7D496 | ses-w96, ses-w0,
2022-11-28 10:25:57,831:INFO:   sub-0391403C | ses-w96, ses-w0,
2022-11-28 10:25:57,831:INFO:   sub-03BCF734 | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:   sub-04550C9F | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:   sub-047D2FA8 | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:   sub-04CB17EC | ses-w96, ses-w0,
2022-11-28 10:25:57,831:INFO:   sub-05A8B309 | ses-w96, ses-w0,
2022-11-28 10:25:57,831:INFO:   sub-06152DED | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:   sub-0693D50B | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:   sub-069B4AC2 | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:   sub-07AB59AD | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:   sub-07E02FCB | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:   sub-07E24E6C | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:   sub-0844A958 | ses-w96, ses-w0,
2022-11-28 10:25:57,831:INFO:   sub-08BB1347 | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:   ...
2022-11-28 10:25:57,831:INFO:   sub-FFCE393E | ses-w0, ses-w96,
2022-11-28 10:25:57,831:INFO:The pipeline will last approximately 10 minutes per image.
Traceback (most recent call last):
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/nipype/utils/spm_docs.py", line 49, in _strip_header
    index = doc.index(hdr)
ValueError: substring not found

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

Traceback (most recent call last):
  File "/workspace/thera/clinicaEnv/bin/clinica", line 8, in <module>
    sys.exit(main())
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/clinica/cmdline.py", line 89, in main
    cli()
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/clinica/pipelines/t1_volume/t1_volume_cli.py", line 91, in cli
    ctx.invoke(
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py", line 68, in cli
    else pipeline.run()
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/clinica/pipelines/engine.py", line 261, in run
    self.build()
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/clinica/pipelines/engine.py", line 25, in func_wrapper
    res = func(self, *args, **kwargs)
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/clinica/pipelines/engine.py", line 232, in build
    self.build_core_nodes()
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_pipeline.py", line 163, in build_core_nodes
    new_segment = npe.Node(spm.NewSegment(), name="2-SpmSegmentation")
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/nipype/interfaces/spm/preprocess.py", line 1873, in __init__
    _local_version = SPMCommand().version
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/nipype/interfaces/spm/base.py", line 310, in __init__
    super(SPMCommand, self).__init__(**inputs)
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 197, in __init__
    unavailable_traits = self._check_version_requirements(
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 295, in _check_version_requirements
    if names and self.version:
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/nipype/interfaces/spm/base.py", line 358, in version
    info_dict = Info.getinfo(
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/nipype/interfaces/spm/base.py", line 239, in getinfo
    out = sd._strip_header(out.runtime.stdout)
  File "/workspace/thera/clinicaEnv/lib/python3.8/site-packages/nipype/utils/spm_docs.py", line 51, in _strip_header
    raise IOError("This docstring was not generated by Nipype!\n") from e
OSError: This docstring was not generated by Nipype!

Do you have any idea about what the problem is ?

I also get the same ValueError when running

from nipype.interfaces import spm
matlab_cmd = ''/opt/spm12/run_spm12.sh /opt/mcr/v97 script''
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
spm.SPMCommand().version

You can find bellow some platform details:

{‘nibabel_version’: ‘2.5.2’,
‘nipype_version’: ‘1.8.5’,
‘numpy_version’: ‘1.23.3’,
‘pkg_path’: ‘/clinicaEnv/lib/python3.8/site-packages/nipype’,
‘scipy_version’: ‘1.9.2’,
‘sys_executable’: ‘/clinicaEnv/bin/python’,
‘sys_platform’: ‘linux’,
‘sys_version’: ‘3.8.5 (default, Jan 27 2021, 15:41:15) \n[GCC 9.3.0]’,
‘traits_version’: ‘6.3.2’}

Thanks a lot for your help !!

[AudreyDuran]

Fixed by setting the FORCE_SPMMCR environment variable (and SPMSTANDALONE_HOME + MCR_HOME variables).
I think that the doc for the set-up in the case of the standalone SPM version could be improved by adding it here :)

[ghisvail]

Indeed, this is inherited from Nipype's design, which is not very well documented. We'll follow your recommendation 👍