Comments (17)
Where is bids-validator located after the Docker file has been created?
2016-08-31 17:57 GMT+02:00 Chris Filo Gorgolewski [email protected]
:
To improve user experience the broccolipipeline.sh script should check if
bids-validator is available and call it (bids-validator $bids_dir) to
check input data compatibility before running any analysis.I'll send a PR to BIDS-App/BROCCOLI updating the Dockerfile to include the
validator.—
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Anders Eklund, PhD
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Done
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Validator fails for ds003 (rhyme judgment)
1: A participants file must have a 'participant_id' column. (code: 48)
/participants.tsv
@ line: 1
Evidence: subject_id sex age
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You must have an outdated version. Can you try with wget
https://googledrive.com/host/0B2JWN60ZLkgkMGlUY3B4MXZIZW8/ds003.tar
On Tue, Sep 6, 2016 at 7:42 AM, Anders Eklund [email protected]
wrote:
Validator fails for ds003 (rhyme judgment)
1: A participants file must have a 'participant_id' column. (code: 48)
/participants.tsv @ line: 1 Evidence: subject_id sex age
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#25 (comment),
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The validator is a nice feature. But in my dataset it detects errors which do not affect my analysis. Is it the case that Broccoli doesnt start if there are BIDS validation errors ? If so, how can I disable the BID validator ?
many thanks
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That would be fabulous! :)
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I'll get an error that the repetition time does not match between scans header and associated JSON files. I don't know the source of this problem but the difference of the TR between files is very small. So it should not affect the analysis....
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...and slice timing info is missing.
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Yes, it seems to be a rounding issue. JSON file TR = 2.58571, header TR = 2.5858.
The BIDS validator integrated in Broccoli tells me the files of all subjects do not match regarding the TR. The online BIDS validator does not detect such an error.....
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Related Issues (20)
- BROCOLLI crashes without error
- TFCE is currently turned off error in RandomiseGroupLevel HOT 4
- permutations tmaps different from fsl randomize output by a factor of ~470 HOT 4
- GLM: segmentation fault HOT 2
- permutations turned off HOT 1
- Memory issue HOT 6
- Registration Failure HOT 1
- output uncorrected results for RandomiseGroupLevel HOT 2
- TFCE support? HOT 2
- AMD gpu and Docker failed HOT 4
- Roadmap? HOT 9
- Error building kernelBayesian.cpp for GPU on macOS HOT 2
- Elastic net regularization for GLM? HOT 2
- RandomiseGroupLevel for repeated measures HOT 2
- RandomiseGroupLevel crashing HOT 5
- python wrapper compilation HOT 1
- Segmentation fault - Multiple runs per participant still not fixed
- Compiling the matlab wrapper on Mac HOT 1
- nipype: BROCCOLI nodes do not produce any output within workflows HOT 1
- Broccoli in WSL2 - Ubuntu 22.04 - HOT 14
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