t1-volume spm standalone error

[Zhangyi Lu]

Hi,

I used Clinica (version 0.9.3) with SPM standalone (version 25.01.02) to run t1-volume, but got the following errors. Can you please advise what is wrong? Thanks.

------------------------

Command lines:

export MCR_HOME=/Applications/MATLAB/MATLAB_Runtime/R2024b

export SPM_HOME=/Users/ninglu/Documents/spm_standalone_25.01.02_macOS_Apple_Silicon/spm_standalone

export SPMSTANDALONE_HOME=/Users/ninglu/Documents/spm_standalone_25.01.02_macOS_Apple_Silicon/spm_standalone

clinica run t1-volume ./ADNI_converted_sample ./ADNI_processed TRAIN -tsv ./ADNI_converted_sample/Train_ADNI.tsv -wd './WD_train' -np 4

-----------------------------

Error logs:

Traceback (most recent call last):

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/bin/clinica", line 8, in <module>

    sys.exit(main())

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/cmdline.py", line 113, in main

    cli()

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1161, in __call__

    return self.main(*args, **kwargs)

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1082, in main

    rv = self.invoke(ctx)

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1697, in invoke

    return _process_result(sub_ctx.command.invoke(sub_ctx))

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1697, in invoke

    return _process_result(sub_ctx.command.invoke(sub_ctx))

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1443, in invoke

    return ctx.invoke(self.callback, **ctx.params)

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 788, in invoke

    return __callback(*args, **kwargs)

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func

    return f(get_current_context(), *args, **kwargs)

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/t1_volume/t1_volume_cli.py", line 95, in cli

    ctx.invoke(

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 788, in invoke

    return __callback(*args, **kwargs)

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py", line 73, in cli

    pipeline.run(plugin="MultiProc", plugin_args={"n_procs": n_procs})

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/engine.py", line 729, in run

    self.build()

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/engine.py", line 45, in func_wrapper

    res = func(self, *args, **kwargs)

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/engine.py", line 690, in build

    self._check_dependencies()

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/pipelines/engine.py", line 798, in _check_dependencies

    dependency.check()

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/utils/check_dependency.py", line 115, in check

    check_software(self.name, log_level="error", specifier=self.version_constraint)

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/utils/check_dependency.py", line 786, in check_software

    _check_software_version(software, log_level=log_level, specifier=specifier)

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/utils/check_dependency.py", line 689, in _check_software_version

    if (installed_version := get_software_version(software)) not in specifier:

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/utils/check_dependency.py", line 518, in get_software_version

    return _get_spm_version()

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/utils/check_dependency.py", line 540, in _get_spm_version

    return Version(spm.SPMCommand().version)

  File "/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/packaging/version.py", line 200, in __init__

    match = self._regex.search(version)

TypeError: expected string or bytes-like object

[Zhangyi Lu]

Hi, 

Can any one take a look at this error. Appreciated it.

Best,

Zhangyi

[Alice Joubert]

Hello Zhangyi, 

I am currently inspecting it.

Best,

Alice

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[Alice Joubert]

Can you try running again without having the `SPM_HOME` variable defined ?

[Zhangyi Lu]

Hi Alice,

Thanks for looking into it. When I only set MCR_HOME and SPMSTANDALONE_HOME. I got "the SPM_HOME variable is not set" error. The following are the detailed logs.

(clinicaEnv) ninglu@Nings-Air ADNI % echo $MCR_HOME                                                                                                                         

/Applications/MATLAB/MATLAB_Runtime/R2024b

(clinicaEnv) ninglu@Nings-Air ADNI % echo $SPMSTANDALONE_HOME

/Users/ninglu/Documents/spm_standalone_25.01.02_macOS_Apple_Silicon/spm_standalone

(clinicaEnv) ninglu@Nings-Air ADNI % echo $SPM_HOME          

(clinicaEnv) ninglu@Nings-Air ADNI % clinica run t1-volume ./ADNI_converted_sample ./ADNI_processed TRAIN -tsv ./ADNI_converted_sample/Train_ADNI.tsv -wd './WD_train' -np 4

2025-03-20 12:55:47,915: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

2025-03-20 12:55:47,915:INFO:Part 1/4: Running t1-volume-segmentation pipeline.

2025-03-20 12:55:47,950:INFO:The CAPS dataset 'None', located at /Users/ninglu/Documents/ADNI/ADNI_processed, already contains a 'dataset_description.json' file.

2025-03-20 12:55:47,951:WARNING:The existing CAPS dataset, located at /Users/ninglu/Documents/ADNI/ADNI_processed has a name 'a5e86e9f-d0cf-448c-af25-cecb21a71c6d' different from the new name '0d8ee856-5329-4e33-a581-e9cf889b81b7'. The old name will be kept.

/Users/ninglu/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/utils/stream.py:103: UserWarning: The existing CAPS dataset, located at /Users/ninglu/Documents/ADNI/ADNI_processed has a name 'a5e86e9f-d0cf-448c-af25-cecb21a71c6d' different from the new name '0d8ee856-5329-4e33-a581-e9cf889b81b7'. The old name will be kept.

  warnings.warn(message, warning_type)

2025-03-20 12:55:47,955:ERROR:Clinica could not find spm software: the SPM_HOME variable is not set.

(clinicaEnv) ninglu@Nings-Air ADNI % 

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[Zhangyi Lu]

Hi Alice,

Hope everything is well. I tried only setting SPMSTANDALONE_HOME, but it still requires SPM_HOME. Do you know what is going on? Thanks.

[Alice Joubert]

Hello, I have investigated further and there are several things that need fixing (see our issue 1481). That might take some time depending on our to-do list and what we decide on. We will try to make it usable again as quickly as possible !

Alice

To view this discussion visit https://groups.google.com/d/msgid/clinica-user/c60658b8-c931-4b1b-9fc5-28d1e1cb6d06n%40googlegroups.com.

[Zhangyi Lu]

Hi Alice. Thank you so much for the update.