Summary of what happened:
I have tried performing an initial preprocessing pipeline using fMRIPrep for data of a single subject, including structural T1- and T2-weighted volumes and rs-fMRI data. However, I get some errors.
Command used (and if a helper script was used, a link to the helper script or the command generated):
fmriprep /home/jovyan/Desktop/dataset/raw /home/jovyan/Desktop/dataset/derivatives participant \
--n_cpus 150 \
--mem_mb 64000 \
--output-spaces fsnative MNI152NLin2009cAsym \
--cifti-output 91k \
--fs-license-file /home/jovyan/Desktop/fmriprep/license.txt \
--skip-bids-validation
Version:
fmriprep 25.1.3
Environment (Docker, Singularity / Apptainer, custom installation):
Via NeuroDesktop.
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/opt/conda/envs/fmriprep/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/fmriprep/cli/workflow.py", line 126, in build_workflow
retval['workflow'] = init_fmriprep_wf()
^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/fmriprep/workflows/base.py", line 95, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/fmriprep/workflows/base.py", line 319, in init_single_subject_wf
anat_fit_wf = init_anat_fit_wf(
^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/niworkflows/engine/splicer.py", line 21, in _tag
node = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/smriprep/workflows/anatomical.py", line 783, in init_anat_fit_wf
anat_template_wf = init_anat_template_wf(
^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/smriprep/workflows/anatomical.py", line 1518, in init_anat_template_wf
StructuralReference(
File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/freesurfer/base.py", line 244, in __init__
super().__init__(**inputs)
File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/freesurfer/base.py", line 134, in __init__
self.inputs.subjects_dir = self._subjects_dir
^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'subjects_dir' trait of a RobustTemplateInputSpec instance must be a pathlike object or string representing an existing directory, but a value of '/home/jovyan/freesurfer-subjects-dir' <class 'str'> was specified.