Hello, Dear Fmriprep community
I was running fmriprep to preprocess data on my local machine MacOS within docker, But there is a problem like this:
RuntimeError: No BOLD images found for participant sub01 and task . All workflows require BOLD images
I have converted neuroimage files into BIDS format and put the bold files within the subdirectory from the input directory
(base) weishao@wei sub-sub01 % ls anat
501_Sub01_sT1W_3D_TFE_32chSHC_20180802141246.json 501_Sub01_sT1W_3D_TFE_32chSHC_20180802141246.nii.gz
(base) weishao@wei sub-sub01 % ls func
201_Sub01_bold_R1.json 201_Sub01_bold_R1.nii.gz 301_Sub01_bold_R2.json 301_Sub01_bold_R2.nii.gz 401_Sub01_bold_R3.json 401_Sub01_bold_R3.nii.gz
(base) weishao@wei sub-sub01 %
Here is my script
#!/bin/bash
export PATH="/Users/weishao/.local/bin:$PATH"
export DOCKER_DEFAULT_PLATFORM=linux/amd64
#User inputs:
bids_root_dir=/Users/weishao/Documents/2020_confidence/Sub01
subj=sub01
nthreads=4
mem=20 #gb
container=docker
#Begin:
#Convert virtual memory from gb to mb
mem=echo "${mem//[!0-9]/}" #remove gb at end
mem_mb=echo $(((mem*1000)-5000)) #reduce some memory for buffer space during pre-processing
#export TEMPLATEFLOW_HOME=$HOME/.cache/templateflow
export FS_LICENSE=/Users/weishao/Documents/2020_confidence/Sub01/license.txt
#Run fmriprep
fmriprep-docker $bids_root_dir $bids_root_dir/derivatives
participant
–participant-label sub-sub01
–skip-bids-validation
–md-only-boilerplate
–fs-license-file /Users/weishao/Documents/2020_confidence/Sub01/license.txt
–fs-no-reconall
–output-spaces MNI152NLin2009cAsym:res-2
–nthreads $nthreads
–stop-on-first-crash
–mem_mb $mem_mb
Here is the output
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.17 -it -v /Users/weishao/Documents/2020_confidence/Sub01/license.txt:/opt/freesurfer/license.txt:ro -v /Users/weishao/Documents/2020_confidence/Sub01:/data:ro -v /Users/weishao/Documents/2020_confidence/Sub01/derivatives:/out nipreps/fmriprep:22.0.0 /data /out participant --participant-label sub-sub01 --skip-bids-validation --md-only-boilerplate --fs-no-reconall --nthreads 4 --stop-on-first-crash --mem_mb 15000 --output-spaces MNI152NLin2009cAsym:res-2
x220808-15:36:47,781 nipype.workflow IMPORTANT:
Running fMRIPrep version 22.0.0
License NOTICE ##################################################
fMRIPrep 22.0.0
Copyright 2022 The NiPreps Developers.
This product includes software developed by
the NiPreps Community (https://nipreps.org/).
Portions of this software were developed at the Department of
Psychology at Stanford University, Stanford, CA, US.
This software redistributes the versioneer Python package, which is
Public domain source code.
This software is also distributed as a Docker container image.
The bootstraping file for the image ("Dockerfile") is licensed
under the MIT License.
This software may be distributed through an add-on package called
"Docker Wrapper" that is under the BSD 3-clause License.
#################################################################
220808-15:37:49,278 nipype.workflow IMPORTANT:
Building fMRIPrep’s workflow:
* BIDS dataset path: /data.
* Participant list: [‘sub01’].
* Run identifier: 20220808-153358_f27b51f2-6b45-46a8-9e66-50ee6a0f2e9b.
* Output spaces: MNI152NLin2009cAsym:res-2.
* Pre-run FreeSurfer’s SUBJECTS_DIR: /out/sourcedata/freesurfer.
Process Process-2:
Traceback (most recent call last):
File “/opt/conda/lib/python3.9/multiprocessing/process.py”, line 315, in _bootstrap
self.run()
File “/opt/conda/lib/python3.9/multiprocessing/process.py”, line 108, in run
self._target(*self._args, **self._kwargs)
File “/opt/conda/lib/python3.9/site-packages/fmriprep/cli/workflow.py”, line 118, in build_workflow
retval[“workflow”] = init_fmriprep_wf()
File “/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/base.py”, line 89, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File “/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/base.py”, line 171, in init_single_subject_wf
raise RuntimeError(
RuntimeError: No BOLD images found for participant sub01 and task . All workflows require BOLD images.