Using fmriprep-docker v1.2.5 I am trying to use the --template-resampling-grid option and give a specific file as an argument (specifically, the MNI152_T1_2mm.nii.gz template included in the HCP pipelines). The file lives on my system on the same partition as the BIDS data, and is rwxrwxr-x, so should be accessible.
It however seems that the file cannot be found by the docker. What am I missing?
Here is the output to the screen:
Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 738, in build_workflow ignore_aroma_err=opts.ignore_aroma_denoising_errors, File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 216, in init_fmriprep_wf ignore_aroma_err=ignore_aroma_err, File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 505, in init_single_subject_wf num_bold=len(subject_data['bold'])) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bold/base.py", line 673, in init_func_preproc_wf name='bold_mni_trans_wf' File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bold/resampling.py", line 335, in init_bold_mni_trans_wf mask_mni_tfm.inputs.reference_image = template_out_grid File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py", line 112, in validate self.info_text, value)) traits.trait_errors.TraitError: The trait 'reference_image' of an ApplyTransformsInputSpec instance is an existing file name, but the path '/data/templates/HCP/MNI152_T1_2mm.nii.gz' does not exist.