Error in DPABISurf when running fMRIPrep

Submitted by Juergen Haenggi on

Dear DPABISurf experts

I try to preprocess rsfMRI data with DPABISurf (DPABI_V7.0_230110) together with the latest docker image and faced the following error with fmriprep:
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You are using fMRIPrep-22.1.1, and a newer version of fMRIPrep is available: 23.0.2.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
--topup-max-vols input is no longer used and the flag will be removed in a future release.

Traceback (most recent call last):

 File "/opt/conda/bin/fmriprep", line 8, in <module>
   sys.exit(main())

 File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/run.py", line 42, in main
   parse_args()

 File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/parser.py", line 810, in parse_args
   validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)

 File "/opt/conda/lib/python3.9/site-packages/fmriprep/utils/bids.py", line 176, 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): 1. Please verify the requested participant labels. This error can be caused by the input data not being accessible inside the docker container. Please make sure all volumes are mounted properly (see https://docs.docker.com/engine/reference/commandline/run/#mount-volume--v---read-only)
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I tested the docker environment by running DPABI->DPABISurf->Utilities->Volume-Surface Projector and it worked.
Directories FunImg and BIDS were created containing .nii and .json files for each subject.
A directory named fmriprep was created containing data from freesurfer.
A directory named fmriprepwork was created containing a subdirectory named 1 that contains 8 subdirectories (4 participants and two attempted runs of fmriprep) named by letter/number strings that each contains a directory bids_db with a file named layout_index.sqlite.
I also validated the BIDS directory and it is a valid BIDS dataset.

I already posted the error in the forum weeks ago but did not get any answers and the post seems to be disappeared from the forum. Hence, I reposted it again.
I appreciate any suggestion how to solve the problem.
Thank you in advance
Kind regards
Jürgen

YAN Chao-Gan

Wed, 07/05/2023 - 12:52

Permalink

Hi Jürgen,

From the message, seems your BIDS data has some problem. You may use DPABISurf start from FunRaw and T1Raw, thus DPABISurf will organize BIDS for you.

Best,

Chao-Gan

Dear Prof. Yan,

thanks a lot for your response. I started with FunRaw and T1Raw and DPABISurf organized the BIDS data for us, but the error occurred. Because the BIDS validator reported some errors and warnings for the BIDS data produced by DPABISurf, I then edited the .json files to correct the error and warnings reported by the BIDS validator and started DPABISurf again using the BIDS directory as starting directory but the error persists.

Any additional idea what can be done to solve the problem is highly appreciated.

Best,

Jürgen

Dear Prof. Yan,

thanks a lot for your response. Please find attached the screenshots of the BIDS data.

I also attached the screenshot of the structure of the fmriprepwork folder.

let me know if you need further information.

Best,

Jürgen

 

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