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wanderine / BROCCOLI

BROCCOLI: Software for Fast fMRI Analysis on Many-Core CPUs and GPUs
GNU General Public License v3.0
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[BIDS] Call validator if available #25

Closed chrisgorgo closed 8 years ago

chrisgorgo commented 8 years ago

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.

wanderine commented 8 years ago

Where is bids-validator located after the Docker file has been created?

2016-08-31 17:57 GMT+02:00 Chris Filo Gorgolewski notifications@github.com :

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

wanderine commented 8 years ago

Done

wanderine commented 8 years ago

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
chrisgorgo commented 8 years ago

You must have an outdated version.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 notifications@github.com 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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NeuroFreakZH commented 7 years ago

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

wanderine commented 7 years ago

Currently it is not possible to turn it off, but I can add an option for that.

2017-03-21 14:50 GMT+01:00 NeuroFreakZH notifications@github.com:

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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-- Anders Eklund, PhD

NeuroFreakZH commented 7 years ago

That would be fabulous! :)

chrisgorgo commented 7 years ago

What errors are you getting?

On Mar 21, 2017 7:07 AM, "NeuroFreakZH" notifications@github.com wrote:

That would be fabulous! :)

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NeuroFreakZH commented 7 years ago

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....

NeuroFreakZH commented 7 years ago

...and slice timing info is missing.

chrisgorgo commented 7 years ago

Could you post the numbers (or the full log)? If it's a rounding error we should look into this.

On Mar 21, 2017 7:54 AM, "NeuroFreakZH" notifications@github.com wrote:

...and slice timing info is missing.

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NeuroFreakZH commented 7 years ago

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.....

chrisgorgo commented 7 years ago

Ah yes I thought we fixed it! All it takes then is for Anders to update the validator in the BROCCOLI BIDS App.

On Mar 21, 2017 8:45 AM, "NeuroFreakZH" notifications@github.com wrote:

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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wanderine commented 7 years ago

And maybe you can guide me to do that ;-)

2017-03-21 16:56 GMT+01:00 Chris Filo Gorgolewski notifications@github.com :

Ah yes I thought we fixed it! All it takes then is for Anders to update the validator in the BROCCOLI BIDS App.

On Mar 21, 2017 8:45 AM, "NeuroFreakZH" notifications@github.com wrote:

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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.

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-- Anders Eklund, PhD

chrisgorgo commented 7 years ago

https://github.com/BIDS-Apps/BROCCOLI/pull/8

wanderine commented 7 years ago

You can now download a new container, which will contain a more recent version of the BIDS validator

docker pull bids/broccoli:v1.0.1

2017-03-21 17:10 GMT+01:00 Anders Eklund andek034@gmail.com:

And maybe you can guide me to do that ;-)

2017-03-21 16:56 GMT+01:00 Chris Filo Gorgolewski < notifications@github.com>:

Ah yes I thought we fixed it! All it takes then is for Anders to update the validator in the BROCCOLI BIDS App.

On Mar 21, 2017 8:45 AM, "NeuroFreakZH" notifications@github.com wrote:

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.....

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/wanderine/BROCCOLI/issues/25#issuecomment-288121363 , or mute the thread https://github.com/notifications/unsubscribe-auth/ AAOkp4dGo1Sr899QrSKHt3-2MRHJc-mdks5rn_CegaJpZM4JxxtH

.

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-- Anders Eklund, PhD

-- Anders Eklund, PhD

NeuroFreakZH commented 7 years ago

Nice. Many thanks! have a good weeken then, michael

Von: Anders Eklund notifications@github.com Gesendet: Donnerstag, 23. März 2017 03:34:44 An: wanderine/BROCCOLI Cc: Meier Michael; Comment Betreff: Re: [wanderine/BROCCOLI] [BIDS] Call validator if available (#25)

You can now download a new container, which will contain a more recent version of the BIDS validator

docker pull bids/broccoli:v1.0.1

2017-03-21 17:10 GMT+01:00 Anders Eklund andek034@gmail.com:

And maybe you can guide me to do that ;-)

2017-03-21 16:56 GMT+01:00 Chris Filo Gorgolewski < notifications@github.com>:

Ah yes I thought we fixed it! All it takes then is for Anders to update the validator in the BROCCOLI BIDS App.

On Mar 21, 2017 8:45 AM, "NeuroFreakZH" notifications@github.com wrote:

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.....

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/wanderine/BROCCOLI/issues/25#issuecomment-288121363 , or mute the thread https://github.com/notifications/unsubscribe-auth/ AAOkp4dGo1Sr899QrSKHt3-2MRHJc-mdks5rn_CegaJpZM4JxxtH

.

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-- Anders Eklund, PhD

-- Anders Eklund, PhD

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