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Corrupted files
Dataset issue
A user reported the following files cannot be opened. This issue is to track investigation and resolution.
Details
ds001241/sub-23/anat/._sub-23_T1w.nii.gz
ds003059/sub-001/anat/._sub-001_T1w.nii.gz
ds003059/sub-002/anat/._sub-002_T1w.nii.gz
ds003059/sub-003/anat/._sub-003_T1w.nii.gz
ds003059/sub-004/anat/._sub-004_T1w.nii.gz
ds003059/sub-006/anat/._sub-006_T1w.nii.gz
ds003059/sub-009/anat/._sub-009_T1w.nii.gz
ds003059/sub-010/anat/._sub-010_T1w.nii.gz
ds003059/sub-011/anat/._sub-011_T1w.nii.gz
ds003059/sub-012/anat/._sub-012_T1w.nii.gz
ds003059/sub-013/anat/._sub-013_T1w.nii.gz
ds003059/sub-015/anat/._sub-015_T1w.nii.gz
ds003059/sub-017/anat/._sub-017_T1w.nii.gz
ds003059/sub-018/anat/._sub-018_T1w.nii.gz
ds003059/sub-019/anat/._sub-019_T1w.nii.gz
ds003059/sub-020/anat/._sub-020_T1w.nii.gz
ds002295/sub-03/ses-anat/anat/sub-03_ses-anat_acq-memp2rage_inv-1_part-mag_MPRAGE.nii.gz
ds002311/sub-02/anat/sub-02_T1w.nii.gz
ds002311/sub-16/anat/sub-16_T1w.nii.gz
ds004146/sub-0162/ses-02/anat/sub-0162_ses-02_UNIT1_denoised.nii.gz
ds002674/sub-01/ses-07/anat/sub-01_ses-07_T2star.nii.gz
ds003707/sub-33/anat/sub-33_T1w.nii.gz
ds003707/sub-33/anat/sub-33_T2w.nii.gz
ds004217/sub-011/anat/sub-011_T1w.nii.gz
ds004217/sub-014/anat/sub-014_T1w.nii.gz
ds004217/sub-018/anat/sub-018_T1w.nii.gz
ds004217/sub-025/anat/sub-025_T1w.nii.gz
ds004217/sub-064/anat/sub-064_T1w.nii.gz
ds004217/sub-070/anat/sub-070_T1w.nii.gz
ds004217/sub-071/anat/sub-071_T1w.nii.gz
ds004217/sub-074/anat/sub-074_T1w.nii.gz
ds004217/sub-077/anat/sub-077_T1w.nii.gz
ds004217/sub-082/anat/sub-082_T1w.nii.gz
ds004217/sub-083/anat/sub-083_T1w.nii.gz
ds004217/sub-084/anat/sub-084_T1w.nii.gz
ds004217/sub-085/anat/sub-085_T1w.nii.gz
ds004217/sub-090/anat/sub-090_T1w.nii.gz
ds004261/sub-2062/ses-day1PM/anat/sub-2062_ses-day1PM_T1w.nii.gz
ds004349/sub-67/anat/sub-67_T1w.nii.gz
ds004349/sub-67/anat/sub-67_T2w.nii.gz
ds004406/sub-02/ses-01/anat/sub-02_ses-01_T1w.nii.gz
ds004406/sub-08/ses-01/anat/sub-08_ses-01_T1w.nii.gz
ds004406/sub-10/ses-01/anat/sub-10_ses-01_T1w.nii.gz
ds004406/sub-17/ses-01/anat/sub-17_ses-01_T1w.nii.gz
ds004406/sub-18/ses-01/anat/sub-18_ses-01_T1w.nii.gz
ds004406/sub-25/ses-01/anat/sub-25_ses-01_T1w.nii.gz
ds004443/sub-0903/ses-01/anat/sub-0903_ses-01_T1w.nii.gz
ds004443/sub-0903/ses-01/anat/sub-0903_ses-01_T2w.nii.gz
ds004482/sub-16/anat/sub-16_T1w.nii.gz
The following datasets are affected
- [ ] ds001241 -
._prefixes, probably just need deleting and re-releasing - [ ] ds003059 -
._prefixes, probably just need deleting and re-releasing - [ ] ds002295 -
sub-03/ses-anat/anat/sub-03_ses-anat_acq-memp2rage_inv-1_part-mag_MPRAGE.nii.gz - [ ] ds002311 - Some T1w images
- [ ] ds004146 -
_UNIT1_denoised:-/ - [ ] ds002674 - T2star
- [ ] ds003707 - Two anatomicals
- [ ] ds004217 - Several T1w images
- [ ] ds004261 - One T1w
- [ ] ds004349 - Two anatomicals
- [ ] ds004406 - Several T1w images
- [ ] ds004443 - Two anatomicals
- [ ] ds004482 - One T1w
ds002345:
root@openneuro-prod-dataset-worker-1:/datasets/ds002345# git annex list | grep -v ^X
here
|github
||s3-PRIVATE
|||s3-PUBLIC
||||web
|||||bittorrent
||||||
___X__ stimuli/santa_audio.wav
___X__ stimuli/shapessocial_audio.wav
___X__ stimuli/sherlock_audio.wav
___X__ stimuli/tunnel_audio.wav
___X__ stimuli/upintheair_audio.wav
___X__ sub-007/func/sub-007_task-pieman_bold.nii.gz
___X__ sub-010/func/sub-010_task-pieman_run-1_bold.nii.gz
___X__ sub-013/func/sub-013_task-pieman_run-2_bold.nii.gz
___X__ sub-017/func/sub-017_task-pieman_bold.nii.gz
___X__ sub-018/anat/sub-018_T1w.nii.gz
___X__ sub-019/anat/sub-019_T1w.nii.gz
___X__ sub-021/anat/sub-021_T1w.nii.gz
___X__ sub-022/anat/sub-022_T1w.nii.gz
@snastase Is there any chance you have the original files for these to re-upload?
Hey @effigies, I just went through and "updated" each of these with the original files through the browser interface on OpenNeuro—do they seem normal now?
@snastase Still seeing these ones missing:
root@openneuro-prod-dataset-worker-1:/datasets/ds002345# git annex list | grep -v ^X
here
|github
||s3-PRIVATE
|||s3-PUBLIC
||||web
|||||bittorrent
||||||
___X__ sub-007/func/sub-007_task-pieman_bold.nii.gz
___X__ sub-010/func/sub-010_task-pieman_run-1_bold.nii.gz
___X__ sub-017/func/sub-017_task-pieman_bold.nii.gz
___X__ sub-018/anat/sub-018_T1w.nii.gz
___X__ sub-019/anat/sub-019_T1w.nii.gz
Hmm okay I tried re-uploading the files more s l o w l y
Did they stick this time? I see the validator error count going down, but there may be other issues.
Looks better. I think some NIfTIs got uploaded as JSON files instead. I'm going to try to revert those...
Okay, the JSON files are reverted. The main complaint now is that there are TRs in the NIfTI headers that don't match the RepetitionTime metadata.
root@openneuro-prod-dataset-worker-1:/datasets/ds002345# nib-ls sub-*/func/*_bold.nii.gz | grep -v 'x1.5'
sub-002/func/sub-002_task-pieman_run-1_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-002/func/sub-002_task-pieman_run-2_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-003/func/sub-003_task-pieman_run-1_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-003/func/sub-003_task-pieman_run-2_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-004/func/sub-004_task-pieman_run-1_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-004/func/sub-004_task-pieman_run-2_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-005/func/sub-005_task-pieman_run-1_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-005/func/sub-005_task-pieman_run-2_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-009/func/sub-009_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-010/func/sub-010_task-pieman_run-1_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-010/func/sub-010_task-pieman_run-2_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-011/func/sub-011_task-pieman_run-1_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-011/func/sub-011_task-pieman_run-2_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-012/func/sub-012_task-pieman_run-1_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-012/func/sub-012_task-pieman_run-2_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-013/func/sub-013_task-pieman_run-1_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-013/func/sub-013_task-pieman_run-2_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-017/func/sub-017_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-018/func/sub-018_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-019/func/sub-019_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-020/func/sub-020_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-021/func/sub-021_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-022/func/sub-022_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-023/func/sub-023_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-024/func/sub-024_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-025/func/sub-025_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-027/func/sub-027_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-028/func/sub-028_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-029/func/sub-029_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-030/func/sub-030_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-031/func/sub-031_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-032/func/sub-032_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-033/func/sub-033_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-034/func/sub-034_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-035/func/sub-035_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-036/func/sub-036_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-037/func/sub-037_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-038/func/sub-038_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-039/func/sub-039_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-040/func/sub-040_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-042/func/sub-042_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-043/func/sub-043_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-044/func/sub-044_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-045/func/sub-045_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-046/func/sub-046_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-047/func/sub-047_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-048/func/sub-048_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-049/func/sub-049_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-050/func/sub-050_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
sub-051/func/sub-051_task-pieman_bold.nii.gz int16 [ 64, 64, 27, 300] 3.00x3.00x4.00x1500.00 sform
That said, those files do also claim their units are ('mm', 'msec'), so this is a validator error. I suppose you can either rewrite the files to use seconds, or we can patch the validator.
Update: https://github.com/bids-standard/bids-specification/pull/2170 resolves these errors.