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20 hours ago •
nipreps
nipreps
mriqc: error: Querying BIDS dataset at </data> got an empty result.
Hi, Dear @oesteban here I run the mriqc, as followed, but it got the error :"mriqc: error: Querying BIDS dataset at got an empty result." PS E:> docker run -it --rm -v /xiuxian/mriqcprocess/nifti:/data:ro -v /xiuxian/mriqcprocess/derivatives:/out poldracklab/mriqc:latest /data /out participant usage: mriqc [-h] [--version] [-v] [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--session-id [SESSION_ID [SESSION_ID ...]]] [--run-id [RUN_ID [RUN_ID ...]]] [--task-id [TASK_ID [TASK_ID ...]]] [-m [MODALITIES [MODALITIES ...]]] [--dsname DSNAME] [--nprocs NPROCS] [--omp-nthreads OMP_NTHREADS] [--mem MEMORY_GB] [--testing] [-f] [--pdb] [-w WORK_DIR] [--verbose-reports] [--write-graph] [--dry-run] [--profile] [--use-plugin USE_PLUGIN] [--no-sub] [--email EMAIL] [--webapi-url WEBAPI_URL] [--webapi-port WEBAPI_PORT] [--upload-strict] [--ants-float] [--ants-settings ANTS_SETTINGS] [--ica] [--fft-spikes-detector] [--fd_thres FD_THRES] [--deoblique] [--despike] [--start-idx START_IDX] [--stop-idx STOP_IDX] [--correct-slice-timing] bids_dir output_dir {participant,group} [{participant,group} ...] mriqc: error: Querying BIDS dataset at got an empty result. Please, check out your currently set filters:
*participant_label: [] *session: None *run: None *task: None *bids_type: None
does anyone know what the problem would be? I used the totally same file folders to run fmriprep, it works. Thank you for suggestion Chen
Hi Chen,
Could you report the output of:
docker run -it --rm -v /xiuxian/mriqcprocess/nifti:/data:ro --entrypoint=find nipreps/mriqc:latest /data -maxdepth 3 -type f
I'm running into this error as well, albeit with slightly different output:
usage: mriqc [-h] [--version] [-v] [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--session-id [SESSION_ID [SESSION_ID ...]]]
[--run-id [RUN_ID [RUN_ID ...]]] [--task-id [TASK_ID [TASK_ID ...]]] [-m [MODALITIES [MODALITIES ...]]] [--dsname DSNAME]
[--nprocs NPROCS] [--omp-nthreads OMP_NTHREADS] [--mem MEMORY_GB] [--testing] [-f] [--pdb] [-w WORK_DIR] [--verbose-reports]
[--write-graph] [--dry-run] [--profile] [--use-plugin USE_PLUGIN] [--no-sub] [--email EMAIL] [--webapi-url WEBAPI_URL]
[--webapi-port WEBAPI_PORT] [--upload-strict] [--ants-float] [--ants-settings ANTS_SETTINGS] [--ica] [--fft-spikes-detector]
[--fd_thres FD_THRES] [--deoblique] [--despike] [--start-idx START_IDX] [--stop-idx STOP_IDX] [--correct-slice-timing]
bids_dir output_dir {participant,group} [{participant,group} ...]
mriqc: error: Querying BIDS dataset at </flywheel/v0/input> got an empty result.
Please, check out your currently set filters:
*participant_label: ['5001', '5002', '5003', '5004', '5005', '5006', '5007', '5009', '5011', '5013', '5014', '5016', '5017', '5018', '5019', '5020', '5021', '5022', '5023', '5024', '5026', '5027', '5028', '5029', '5032', '5033', '5034', '5035', '5037', '5038', '5039', '5040', '5041', '5042', '5043', '5044', '5045', '5046', '5047', '5049', '5050', '5051', '5052', '5053', '5054', '5056', '5058', '5059', '5060', '5061', '5062', '5063', '6002', '6003', '6004', '6005', '6006', '6007', '6009', '6011', '6012', '6013', '6014', '6016', '6017', '6018', '6019', '6020', '6021', '6022', '6023', '6025', '6027', '6028', '6029', '6030', '6031', '6032', '6033', '6034', '6037', '6038', '6039', '6040', '6041', '6042', '6043', '6044', '6045', '6046', '6048', '6049', '6052', '6053', '7003', '7004', '7010', '7012', '7013', '7014', '7016', '7017', '7018', '7019', '7021', '7022', '7023', '7025', '7026', '7027', '7028', '7030', '7031', '8001', '8002', '8003', '8004', '8006', '8008', '8009', '8010', '8011', '8013', '8014', '8015', '8016', '8017', '8018', '8019', '8020', '8022', '8023', '8026', '8028', '8029', '8030', '8031']
*session: None
*run: None
*task: None
*bids_type: None
From the "participant_label" section of the error it seems clear that it's finding the participant folders, but evidently it's not finding what it wants beyond that.
A find command of maxdepth 3 returns nothing, but here's the output when I boost maxdepth to 4:
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
MacBook-Air-2:mriqc noah$ docker run -i -t --rm -v /flywheel-test/mriqc/input:/flywheel/v0 --entrypoint=find poldracklab/mriqc:0.16.1 /flywheel/v0 -maxdepth 4 -type f
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
/flywheel/v0/sub-5001/ses-post/func/sub-5001_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5001/ses-post/func/sub-5001_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5001/ses-post/func/sub-5001_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5002/ses-post/func/sub-5002_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5002/ses-post/func/sub-5002_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5002/ses-post/func/sub-5002_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5003/ses-post/func/sub-5003_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5003/ses-post/func/sub-5003_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5003/ses-post/func/sub-5003_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5004/ses-post/func/sub-5004_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5004/ses-post/func/sub-5004_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5004/ses-post/func/sub-5004_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5005/ses-post/func/sub-5005_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5005/ses-post/func/sub-5005_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5005/ses-post/func/sub-5005_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5006/ses-post/func/sub-5006_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5006/ses-post/func/sub-5006_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5006/ses-post/func/sub-5006_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5007/ses-post/func/sub-5007_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5007/ses-post/func/sub-5007_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5007/ses-post/func/sub-5007_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5009/ses-post/func/sub-5009_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5009/ses-post/func/sub-5009_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5009/ses-post/func/sub-5009_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5011/ses-post/func/sub-5011_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5011/ses-post/func/sub-5011_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5011/ses-post/func/sub-5011_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5013/ses-post/func/sub-5013_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5013/ses-post/func/sub-5013_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5013/ses-post/func/sub-5013_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5014/ses-post/func/sub-5014_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5014/ses-post/func/sub-5014_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5014/ses-post/func/sub-5014_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5016/ses-post/func/sub-5016_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5016/ses-post/func/sub-5016_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5016/ses-post/func/sub-5016_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5017/ses-post/func/sub-5017_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5017/ses-post/func/sub-5017_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5017/ses-post/func/sub-5017_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5018/ses-post/func/sub-5018_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5018/ses-post/func/sub-5018_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5018/ses-post/func/sub-5018_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5019/ses-post/func/sub-5019_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5019/ses-post/func/sub-5019_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5019/ses-post/func/sub-5019_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5020/ses-post/func/sub-5020_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5020/ses-post/func/sub-5020_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5020/ses-post/func/sub-5020_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5021/ses-post/func/sub-5021_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-5021/ses-post/func/sub-5021_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5021/ses-post/func/sub-5021_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5022/ses-post/func/sub-5022_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5022/ses-post/func/sub-5022_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5022/ses-post/func/sub-5022_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5023/ses-post/func/sub-5023_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5023/ses-post/func/sub-5023_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5023/ses-post/func/sub-5023_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5024/ses-post/func/sub-5024_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5024/ses-post/func/sub-5024_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5024/ses-post/func/sub-5024_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5026/ses-post/func/sub-5026_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5026/ses-post/func/sub-5026_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5026/ses-post/func/sub-5026_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5027/ses-post/func/sub-5027_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5027/ses-post/func/sub-5027_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5027/ses-post/func/sub-5027_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5028/ses-post/func/sub-5028_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5028/ses-post/func/sub-5028_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5028/ses-post/func/sub-5028_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5029/ses-post/func/sub-5029_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5029/ses-post/func/sub-5029_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5029/ses-post/func/sub-5029_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5032/ses-post/func/sub-5032_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5032/ses-post/func/sub-5032_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5032/ses-post/func/sub-5032_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5033/ses-post/func/sub-5033_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5033/ses-post/func/sub-5033_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5033/ses-post/func/sub-5033_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5034/ses-post/func/sub-5034_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5034/ses-post/func/sub-5034_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5034/ses-post/func/sub-5034_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5035/ses-post/func/sub-5035_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5035/ses-post/func/sub-5035_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5035/ses-post/func/sub-5035_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5037/ses-post/func/sub-5037_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5037/ses-post/func/sub-5037_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5037/ses-post/func/sub-5037_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5038/ses-post/func/sub-5038_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5038/ses-post/func/sub-5038_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5038/ses-post/func/sub-5038_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5039/ses-post/func/sub-5039_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5039/ses-post/func/sub-5039_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5039/ses-post/func/sub-5039_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5040/ses-post/func/sub-5040_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5040/ses-post/func/sub-5040_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5040/ses-post/func/sub-5040_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5041/ses-post/func/sub-5041_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5041/ses-post/func/sub-5041_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5041/ses-post/func/sub-5041_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5042/ses-post/func/sub-5042_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5042/ses-post/func/sub-5042_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5042/ses-post/func/sub-5042_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5043/ses-post/func/sub-5043_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5043/ses-post/func/sub-5043_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5043/ses-post/func/sub-5043_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5044/ses-post/func/sub-5044_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5044/ses-post/func/sub-5044_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5044/ses-post/func/sub-5044_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5045/ses-post/func/sub-5045_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5045/ses-post/func/sub-5045_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5045/ses-post/func/sub-5045_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5046/ses-post/func/sub-5046_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5046/ses-post/func/sub-5046_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5046/ses-post/func/sub-5046_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5047/ses-post/func/sub-5047_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5047/ses-post/func/sub-5047_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5047/ses-post/func/sub-5047_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5049/ses-post/func/sub-5049_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-5049/ses-post/func/sub-5049_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5049/ses-post/func/sub-5049_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5050/ses-post/func/sub-5050_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5050/ses-post/func/sub-5050_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5050/ses-post/func/sub-5050_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5051/ses-post/func/sub-5051_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-5051/ses-post/func/sub-5051_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5051/ses-post/func/sub-5051_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5052/ses-post/func/sub-5052_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5052/ses-post/func/sub-5052_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5052/ses-post/func/sub-5052_ses-post_task-ultimatumGame_echo-3_bold.json
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/flywheel/v0/sub-5053/ses-post/func/sub-5053_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5053/ses-post/func/sub-5053_ses-post_task-ultimatumGame_echo-3_bold.json
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/flywheel/v0/sub-5054/ses-post/func/sub-5054_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5054/ses-post/func/sub-5054_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5056/ses-post/func/sub-5056_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-5056/ses-post/func/sub-5056_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-5056/ses-post/func/sub-5056_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-5058/ses-post/func/sub-5058_ses-post_task-ultimatumGame_echo-1_bold.json
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/flywheel/v0/sub-5058/ses-post/func/sub-5058_ses-post_task-ultimatumGame_echo-3_bold.json
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/flywheel/v0/sub-7028/ses-post/func/sub-7028_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-7030/ses-post/func/sub-7030_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-7030/ses-post/func/sub-7030_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-7030/ses-post/func/sub-7030_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-7031/ses-post/func/sub-7031_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-7031/ses-post/func/sub-7031_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-7031/ses-post/func/sub-7031_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8001/ses-post/func/sub-8001_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8001/ses-post/func/sub-8001_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8001/ses-post/func/sub-8001_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8002/ses-post/func/sub-8002_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8002/ses-post/func/sub-8002_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8002/ses-post/func/sub-8002_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8003/ses-post/func/sub-8003_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8003/ses-post/func/sub-8003_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8003/ses-post/func/sub-8003_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8004/ses-post/func/sub-8004_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8004/ses-post/func/sub-8004_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8004/ses-post/func/sub-8004_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8006/ses-post/func/sub-8006_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8006/ses-post/func/sub-8006_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8006/ses-post/func/sub-8006_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8008/ses-post/func/sub-8008_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8008/ses-post/func/sub-8008_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8008/ses-post/func/sub-8008_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8009/ses-post/func/sub-8009_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8009/ses-post/func/sub-8009_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8009/ses-post/func/sub-8009_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8010/ses-post/func/sub-8010_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8010/ses-post/func/sub-8010_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8010/ses-post/func/sub-8010_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8011/ses-post/func/sub-8011_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8011/ses-post/func/sub-8011_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8011/ses-post/func/sub-8011_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8013/ses-post/func/sub-8013_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8013/ses-post/func/sub-8013_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8013/ses-post/func/sub-8013_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8014/ses-post/func/sub-8014_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8014/ses-post/func/sub-8014_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8014/ses-post/func/sub-8014_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8015/ses-post/func/sub-8015_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8015/ses-post/func/sub-8015_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8015/ses-post/func/sub-8015_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8016/ses-post/func/sub-8016_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8016/ses-post/func/sub-8016_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8016/ses-post/func/sub-8016_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8017/ses-post/func/sub-8017_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8017/ses-post/func/sub-8017_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8017/ses-post/func/sub-8017_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8018/ses-post/func/sub-8018_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8018/ses-post/func/sub-8018_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8018/ses-post/func/sub-8018_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8019/ses-post/func/sub-8019_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8019/ses-post/func/sub-8019_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8019/ses-post/func/sub-8019_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8020/ses-post/func/sub-8020_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8020/ses-post/func/sub-8020_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8020/ses-post/func/sub-8020_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8022/ses-post/func/sub-8022_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8022/ses-post/func/sub-8022_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8022/ses-post/func/sub-8022_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8023/ses-post/func/sub-8023_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8023/ses-post/func/sub-8023_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8023/ses-post/func/sub-8023_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8026/ses-post/func/sub-8026_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8026/ses-post/func/sub-8026_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8026/ses-post/func/sub-8026_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8028/ses-post/func/sub-8028_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8028/ses-post/func/sub-8028_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8028/ses-post/func/sub-8028_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8029/ses-post/func/sub-8029_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8029/ses-post/func/sub-8029_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8029/ses-post/func/sub-8029_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8030/ses-post/func/sub-8030_ses-post_task-ultimatumGame_echo-1_bold.json
/flywheel/v0/sub-8030/ses-post/func/sub-8030_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8030/ses-post/func/sub-8030_ses-post_task-ultimatumGame_echo-3_bold.json
/flywheel/v0/sub-8031/ses-post/func/sub-8031_ses-post_task-ultimatumGame_bold.json
/flywheel/v0/sub-8031/ses-post/func/sub-8031_ses-post_task-ultimatumGame_echo-2_bold.json
/flywheel/v0/sub-8031/ses-post/func/sub-8031_ses-post_task-ultimatumGame_echo-3_bold.json
@oesteban - Any suggestions on where else I can look to help track down this problem?
No. I see now that I didn't include my command above, but this is for a group report:
docker run -i -t --rm -v/Users/noah/Documents/code/usc/flywheel-test/mriqc:/flywheel/v0 poldracklab/mriqc:latest /flywheel/v0/input /flywheel/v0/output group
In the past (iirc), group reports only needed the .json files generated by the individual reports, not the underlying niftis. Is that no longer the case? (Or am I completely misremembering the way it used to work? It's been a while since I used mriqc.)
We're running into this same issue as well - but we only have niftis, no jsons. Is that a problem?
@noah10 I think you are not providing the original data folder to the group subcommand.
@dmd - can you give more details of what command you are running and the contents of the input and output folder (at least to see what can be the problem).
We run:
singularity exec -B /data/skohut /cm/shared/singularity/images/mriqc-latest.sif mriqc /data/skohut/data/cathinone /data/skohut/data/cathinone/quality participant --no-sub -w /data/skohut/work
Here are the contents of /data/skohut/data/cathinone
Okay, I think the problem is that /data/skohut/data/cathinone contains not just the original data, but also results from other workflows and mriqc participant results. Then, PyBIDS tries to index all of that. I believe you want to add a .bidsignore file clarifying what to index to MRIQC or separate original and derivatives data.
I don't think there's a particular bug to be addressed here that grants the blocking of the 22 release. I'm going to remove the milestone and continue checking with @dmd @noah10 to determine whether there is a bug or it's just a problem with nonconformant BIDS structures.
@oesteban Are you saying that in a command like this:
docker run -i -t --rm -v/Users/noah/Documents/code/usc/flywheel-test/mriqc:/flywheel/v0
poldracklab/mriqc:latest /flywheel/v0/input /flywheel/v0/output group
... the /flywheel/v0/input folder should contain both the original nifti's as well as the .json files generated by the individual reports? Or is there some alternate syntax where I specify an input folder with the nifti's, an input folder with the .json files and an output folder?
@noah10 MRIQC has a BIDS-Apps interface, which means the command line is:
mriqc <input-BIDS-root> <derivatives-path> participant
or
mriqc <input-BIDS-root> <derivatives-path> group
In both cases, <input-BIDS-root> should point at the original (as in raw, or unprocessed) data in BIDS and this BIDS dataset should be valid. Therefore, poluting the folder structure with extraneous files will just confuse MRIQC.
In both cases, <derivatives-path> is the output, and should point to the same folder in both steps. First, the participant level will fill this <derivatives-path> with the metrics and reports corresponding to each input subject and then group will read those in and generate the group report. Again, poluting this directory with other contents will definitely confuse MRIQC
For whatever it's worth, I was consistently getting this error with 22.0.0 running in docker when I used --session-id with a session ID that included the "ses-" prefix (e.g., --session-id ses-visit1). Dropping the "-ses" prefix resolved it for me. This was mostly user error: I'd assumed it worked like --participant_label, but the parser doesn't yet have a _drop_ses function analogous to _drop_sub.
We are going to consider this issue abandoned. If someone hits the same problem and none of the solutions above work out, please reopen.
There seems to be a regression in 23.0.0.
Using this command:
singularity exec -B /data/skohut/data /cm/shared/singularity/images/mriqc-23.0.0.sif mriqc /data/skohut/data/thc2 /data/skohut/data/thc2/quality participant --no-sub
We get:
mriqc: error: Querying BIDS dataset at </data/skohut/data/thc2> got an empty result.
Please, check out your currently set filters:
*participant_label: []
*session: None
*run: None
*task: None
*bids_type: None
However, running the exact same command but using mriqc-22.0.6.sif succeeds.
Here is the directory structure:
[hleblanc@micc hleblanc]$ find /data/skohut/data/thc2
/data/skohut/data/thc2
/data/skohut/data/thc2/template_part1_post.fsf
/data/skohut/data/thc2/sub-ss34F
/data/skohut/data/thc2/sub-ss34F/ses-21chronic
/data/skohut/data/thc2/sub-ss34F/ses-21chronic/func
/data/skohut/data/thc2/sub-ss34F/ses-21chronic/func/sub-ss34F_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/template_part2.fsf
/data/skohut/data/thc2/template_part1_pre.fsf
/data/skohut/data/thc2/sub-ss26
/data/skohut/data/thc2/sub-ss26/ses-22chronic
/data/skohut/data/thc2/sub-ss26/ses-22chronic/func
/data/skohut/data/thc2/sub-ss26/ses-22chronic/func/sub-ss26_ses-22chronic_task-rest_bold.nii
/data/skohut/data/thc2/sub-ss26/ses-21chronic
/data/skohut/data/thc2/sub-ss26/ses-21chronic/func
/data/skohut/data/thc2/sub-ss26/ses-21chronic/func/sub-ss26_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/sub-ss22
/data/skohut/data/thc2/sub-ss22/ses-21chronic
/data/skohut/data/thc2/sub-ss22/ses-21chronic/func
/data/skohut/data/thc2/sub-ss22/ses-21chronic/func/sub-ss22_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/preproc
/data/skohut/data/thc2/sub-ss35F
/data/skohut/data/thc2/sub-ss35F/ses-21chronic
/data/skohut/data/thc2/sub-ss35F/ses-21chronic/func
/data/skohut/data/thc2/sub-ss35F/ses-21chronic/func/sub-ss35F_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/template_part1_pharma.fsf
/data/skohut/data/thc2/sub-ss32F
/data/skohut/data/thc2/sub-ss32F/ses-21chronic
/data/skohut/data/thc2/sub-ss32F/ses-21chronic/func
/data/skohut/data/thc2/sub-ss32F/ses-21chronic/func/sub-ss32F_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/sub-ss25
/data/skohut/data/thc2/sub-ss25/ses-21chronic
/data/skohut/data/thc2/sub-ss25/ses-21chronic/func
/data/skohut/data/thc2/sub-ss25/ses-21chronic/func/sub-ss25_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/dataset_description.json
/data/skohut/data/thc2/sub-ss27
/data/skohut/data/thc2/sub-ss27/ses-21chronic
/data/skohut/data/thc2/sub-ss27/ses-21chronic/func
/data/skohut/data/thc2/sub-ss27/ses-21chronic/func/sub-ss27_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/sub-ss20
/data/skohut/data/thc2/sub-ss20/ses-21chronic
/data/skohut/data/thc2/sub-ss20/ses-21chronic/func
/data/skohut/data/thc2/sub-ss20/ses-21chronic/func/sub-ss20_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/sub-ss36F
/data/skohut/data/thc2/sub-ss36F/ses-21chronic
/data/skohut/data/thc2/sub-ss36F/ses-21chronic/func
/data/skohut/data/thc2/sub-ss36F/ses-21chronic/func/sub-ss36F_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/sub-ss24
/data/skohut/data/thc2/sub-ss24/ses-21chronic
/data/skohut/data/thc2/sub-ss24/ses-21chronic/func
/data/skohut/data/thc2/sub-ss24/ses-21chronic/func/sub-ss24_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/sub-ss24/ses-22chronic
/data/skohut/data/thc2/sub-ss24/ses-22chronic/func
/data/skohut/data/thc2/sub-ss24/ses-22chronic/func/sub-ss24_ses-22chronic_task-rest_bold.nii
/data/skohut/data/thc2/template_part1.fsf
/data/skohut/data/thc2/sub-ss37F
/data/skohut/data/thc2/sub-ss37F/ses-21chronic
/data/skohut/data/thc2/sub-ss37F/ses-21chronic/func
/data/skohut/data/thc2/sub-ss37F/ses-21chronic/func/sub-ss37F_ses-21chronic_task-rest_bold.nii
/data/skohut/data/thc2/template_part1_rest.fsf
@dmd this seems to be related to the sessions bit, I will keep this one closed - but please follow up on #1086.
Thanks for the file tree - I'll write a unit test with it if you don't mind, to ensure this will work with your structure.