Fmriprep error while creating initial workflows



I’m using fmriprep with a Docker container and have preprocessed several test datasets. Today I ran the command as I always have and encountered an error almost immediately after the command started running, while fmriprep is creating the initial workflows, etc. Here is my command and error message:

$ sudo docker run -ti --rm -v /path/to/data:/data:ro -v /path/to/output/folder:/out poldracklab/fmriprep:latest /data /out/out participant --no-freesurfer --low-mem
Unable to find image ‘poldracklab/fmriprep:latest’ locally
latest: Pulling from poldracklab/fmriprep
b3e1c725a85f: Pull complete
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399dd80b26b2: Pull complete
Digest: sha256:c9c2a5bbb4350275bcf33777c014aa89724372892618cc5128fc7187b30d68e6
Status: Downloaded newer image for poldracklab/fmriprep:latest
171031-22:19:59,825 cli INFO:

Running fMRIPREP version 0.6.8:

  • Participant list: [‘01’, ‘02’, ‘03’, ‘04’, ‘05’, ‘06’, ‘07’, ‘08’, ‘09’, ‘10’].
  • Run identifier: 20171031-221959_b4ecc041-6f9b-412c-87c1-296d7ed29263.

Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 11, in
load_entry_point(‘fmriprep==0.6.8’, ‘console_scripts’, ‘fmriprep’)()
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/”, line 214, in main
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/”, line 326, in create_workflow
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/”, line 189, in init_fmriprep_wf
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/”, line 430, in init_single_subject_wf
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/”, line 261, in init_func_preproc_wf
run_stc = (“SliceTiming” in metadata and
TypeError: argument of type ‘NoneType’ is not iterable

The ‘Unable to find image ‘poldracklab/fmriprep:latest’ locally’ was probably because I changed some of my Docker settings, which can delete old images. But I reset all of the settings on my Docker build (back to what I had successfully used many times) and still got the same error. If anyone thinks it might be a Docker-specific problem, here is my info:

$ sudo docker info
Containers: 0
Running: 0
Paused: 0
Stopped: 0
Images: 1
Server Version: 17.09.0-ce
Storage Driver: aufs
Root Dir: /var/lib/docker/aufs
Backing Filesystem: extfs
Dirs: 48
Dirperm1 Supported: false
Logging Driver: json-file
Cgroup Driver: cgroupfs
Volume: local
Network: bridge host macvlan null overlay
Log: awslogs fluentd gcplogs gelf journald json-file logentries splunk syslog
Swarm: inactive
Runtimes: runc
Default Runtime: runc
Init Binary: docker-init
containerd version: 06b9cb35161009dcb7123345749fef02f7cea8e0
runc version: 3f2f8b84a77f73d38244dd690525642a72156c64
init version: 949e6fa
Security Options:
Kernel Version: 3.13.0-135-generic
Operating System: Ubuntu 14.04.5 LTS
OSType: linux
Architecture: x86_64
CPUs: 8
Total Memory: 31.3GiB
Name: mufasa
Docker Root Dir: /var/lib/docker
Debug Mode (client): false
Debug Mode (server): false
Experimental: false
Insecure Registries:
Live Restore Enabled: false

Any insight would be greatly appreciated!


What is the content of the JSON sidecar for a bold run (any of them)?


Is your dataset passing the validator: ?


Thanks for your response and sorry for getting back to you late. My data was all fine but my *task_bold.json files weren’t formatted correctly. Fixing those did it. Thanks for your help.