pb of "path not tuple" during t1-volume-dartel2mni

[ccLiiFE]

Hi,
First thanks a lot for this tool, it will save me a lot of time in the future.
However, right now I am struggling with the session t1-volume-dartel2mni of the pipeline T1 volume.

Here is my terminal output (I am using only two T1 for the moment it was to see if everything was fine):
//-----------------------------------------------
2023-03-28 11:57:48,117:INFO:The pipeline will be run on the following 2 image(s):
2023-03-28 11:57:48,117:INFO: sub-207004 | ses-M00,
2023-03-28 11:57:48,117:INFO: sub-207032 | ses-M00,
2023-03-28 11:57:48,117:INFO:The pipeline will last a few minutes per image.

Traceback (most recent call last):
File "/mnt/software/miniconda3/envs/clinicaEnv/bin/clinica", line 8, in
sys.exit(main())
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/clinica/cmdline.py", line 92, in main
cli()
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_cli.py", line 67, in cli
pipeline.run(plugin="MultiProc", plugin_args={"n_procs": n_procs})
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/clinica/pipelines/engine.py", line 339, in run
raise e
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/clinica/pipelines/engine.py", line 320, in run
exec_graph = Workflow.run(self, plugin, plugin_args, update_hash)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 166, in run
self._clean_queue(jobid, graph, result=result)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 244, in _clean_queue
raise RuntimeError("".join(result["traceback"]))
RuntimeError: Traceback (most recent call last):
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
return self._run_command(execute)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _unzip_tissues_node0.

Traceback (most recent call last):
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
out = function_handle(**args)
File "", line 43, in unzip_nii
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/site-packages/clinica/utils/filemanip.py", line 21, in _zip_unzip_nii
in_file = Path(in_file)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/pathlib.py", line 1046, in new
self = cls._from_parts(args, init=False)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/pathlib.py", line 687, in _from_parts
drv, root, parts = self._parse_args(args)
File "/mnt/software/miniconda3/envs/clinicaEnv/lib/python3.8/pathlib.py", line 671, in _parse_args
a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not tuple
//-----------------------------------------------------

I try to plot this famous "a" from the os.fpath(a) and indeed I have a tuple: the 3 segmentations files for each my two subjects

---

('/NAS/tupac/cecile/TryClinica/data/Results/subjects/sub-207004/ses-M00/t1/spm/segmentation/native_space/sub-207004_ses-0_acq-301s3DT15MIN3D_T1w_segm-graymatter_probability.nii.gz', '/NAS/tupac/cecile/TryClinica/data/Results/subjects/sub-207004/ses-M00/t1/spm/segmentation/native_space/sub-207004_ses-0_acq-301s3DT15MIN3D_T1w_segm-whitematter_probability.nii.gz', '/NAS/tupac/cecile/TryClinica/data/Results/subjects/sub-207004/ses-M00/t1/spm/segmentation/native_space/sub-207004_ses-0_acq-301s3DT15MIN3D_T1w_segm-csf_probability.nii.gz')

---

---

('/NAS/tupac/cecile/TryClinica/data/Results/subjects/sub-207032/ses-M00/t1/spm/segmentation/native_space/sub-207032_ses-0_acq-301s3DT15MIN3D_T1w_segm-graymatter_probability.nii.gz', '/NAS/tupac/cecile/TryClinica/data/Results/subjects/sub-207032/ses-M00/t1/spm/segmentation/native_space/sub-207032_ses-0_acq-301s3DT15MIN3D_T1w_segm-whitematter_probability.nii.gz', '/NAS/tupac/cecile/TryClinica/data/Results/subjects/sub-207032/ses-M00/t1/spm/segmentation/native_space/sub-207032_ses-0_acq-301s3DT15MIN3D_T1w_segm-csf_probability.nii.gz')

---

Am I missing something? did somebody get the same pb?
I have to admit I have no idea how to resolve this pb, should not the files be all preprocessed separately?

Thanks a lot for your help!
Cecile

[ccLiiFE]

Sorry I found the pb in the issues.
Thx