Fmriprep: Each element of the 'input_image' trait of a DynamicTraitedSpec instance must be a pathlike object or string representing an existing file Error

Software Support
1

Summary of what happened:

Hi im trying to run fmriprep and I encountered this issue.

input data is BIDS-validated, I make sure of it.

What is the reason of this issue? and How should I solve this? Please lemme know.

Best,

JunYong Oh

Command used (and if a helper script was used, a link to the helper script or the command generated):

#User inputs:
bids_root_dir=$HOME/Desktop/bids_output
subj=01
nthreads=4
container=docker #docker or singularity



fmriprep-docker $bids_root_dir $bids_root_dir/fmriprep \
  participant \
    --participant-label $subj \
    --skip-bids-validation \
    --md-only-boilerplate \
    --fs-license-file $HOME/Downloads/license.txt \
    --fs-no-reconall \
    --output-spaces MNI152NLin2009cAsym:res-2 \
    --nthreads $nthreads \
    --stop-on-first-crash \
    --mem_mb 12000 \
    -w $HOME

Version:

Environment (Docker, Singularity / Apptainer, custom installation):

Docker

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Data formatted according to a validatable standard? Please provide the output of the validator:

yes it is validated(Used BIDS validator)

2

Hi @dhwnsdyd21,

Please use the software support post category, which gives you a post template to fill in. This gives us information that can help us help you. You can see I added it in for you this time. You can edit your post to add missing information in. It would also be good to know how much memory/cpus you are using for fmriprep.

Best,
Steven

3

Thank you for your recommendation!!

Sincerely,
Junyong Oh

4

Hi @dhwnsdyd21,

Thanks for the info, but it’s still unclear what version you used. Also, I would try to increase the memory if you can. Is this error subject specific or does it happen to other subjects in your dataset?

Best,
Steven