I am getting a following error for alreday bids-validated data.
RuntimeError: Data for requested participant(s) label(s) not found. Could not find data for participant(s): 50050. Please verify the requested participant labels. This error can be caused by the input data not being accessible inside the singularity container. Please make sure all paths are mapped properly
Please let me know how to fix this issue. Thanks in advance.
Assuming that /gpfs/projects/fmriprep/my_data/sub-50050 exists and contains a T1w file, then the likely issue is that the path isn’t mapped inside the Singularity container. Try:
$ singularity shell /gpfs/software/fmriprep-1.5.5/fmriprep-1.5.5.simg
> ls /gpfs/projects/fmriprep/my_data
If your dataset is accessible, it should look normal. If it is not, then it may error and say that the directory doesn’t exist or show an empty directory.
(Note that the sub- on the argument to --participant-label is not following with the BIDS-Apps convention, but fMRIPrep automatically removes the sub-, so removing it will have no effect.)
Some parts of fMRIPrep may fail to complete.
Continue anyway? [y/N]y
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.13 -it -v /mnt/c/Users/rubin/fs-license/license.txt:/opt/freesurfer/license.txt:ro -v /mnt/c/Users/rubin/derivatives:/data:ro -v /mnt/c/Users/rubin/fs-license/participant:/out -v /mnt/c/Users/rubin/BIDS:/scratch nipreps/fmriprep:20.2.2 /data /out participant --participant-label sub-A0123061 --low-mem -w /scratch --output-spaces MNI152NLin6Asym
You are using fMRIPrep-20.2.2, and a newer version of fMRIPrep is available: 21.0.1.
Please check out our documentation about how and when to upgrade: https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 10, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 17, in main
parse_args()
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py”, line 711, in parse_args
config.environment.exec_env, opts.bids_dir, opts.participant_label
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/utils/bids.py”, line 145, in validate_input_dir
raise RuntimeError(error_msg % ‘,’.join(bad_labels))
RuntimeError: Data for requested participant(s) label(s) not found. Could not find data for participant(s): A0123061. Please verify the requested participant labels.
That --w argument is messing things up. I don’t know what it is supposed to be a variable for, did you mean to do -w instead? -w is where you specify a work directory. Try this instead.
However, now I get other errors (please see below)
Traceback (most recent call last):
File “/opt/conda/bin/fmriprep”, line 8, in
sys.exit(main())
File “/opt/conda/lib/python3.8/site-packages/fmriprep/cli/run.py”, line 38, in main
parse_args()
File “/opt/conda/lib/python3.8/site-packages/fmriprep/cli/parser.py”, line 679, in parse_args
config.from_dict(vars(opts))
File “/opt/conda/lib/python3.8/site-packages/fmriprep/config.py”, line 666, in from_dict
execution.load(settings)
File “/opt/conda/lib/python3.8/site-packages/fmriprep/config.py”, line 238, in load
cls.init()
File “/opt/conda/lib/python3.8/site-packages/fmriprep/config.py”, line 481, in init
cls._layout = BIDSLayout(
File “/opt/conda/lib/python3.8/site-packages/bids/layout/layout.py”, line 126, in init
root, description = validate_root(root, validate)
File “/opt/conda/lib/python3.8/site-packages/bids/layout/validation.py”, line 73, in validate_root
raise BIDSValidationError(
bids.exceptions.BIDSValidationError: ‘dataset_description.json’ is missing from project root. Every valid BIDS dataset must have this file.
Example contents of ‘dataset_description.json’:
{“Name”: “Example dataset”, “BIDSVersion”: “1.0.2”}
fMRIPrep: Please report errors to Issues · nipreps/fmriprep · GitHub
I do have ‘dataset_description.json’ file but the code still fails
Thank you, will change the working directory to another one that is not the same as BIDS.
Yes, I was using a working directory with an older version of fMRIPrep. Does this mean that I have to run it again from scratch since I updated fMRIPrep?
The data is BIDS valid.
The contents of the dataset description file is as follows:
{
“Name”: " ",
“BIDSVersion”: “1.4.0”,
“DatasetType”: “raw”,
“Authors”: [
“Please cite MNE-BIDS in your publication before removing this (citations in README)”
]
}
Yes. If you want to use the older version, you can use the same command to run fmriprep, but I wouldn’t recommend it unless you need to use that older version. Also, keep in mind if you use the new version, that the output layout will be different than version 20.X.X. If you want the output layout to be the same as 20.X.X you can also add the argument --output-layout legacy.
When I try to run the code using a working directory to re-process some data, I get prompted to update to a newer version of fMRIPrep so I updated it to 21.0.1. I’ll use that argument after the code.
I’m still getting the same error with the dataset description file. Is there something regarding the contents of the file that I need to modify?
