[BIDS] Call validator if available about broccoli

[wanderine]

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

[wanderine]

Done

[wanderine]

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]

You must have an outdated version.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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[NeuroFreakZH]

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]

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 <[email protected]>:

…

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 — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEGryDZHUW7Sdsh7rCMCCyuplwk4D3n7ks5rn9WwgaJpZM4JxxtH> .

-- Anders Eklund, PhD

[NeuroFreakZH]

That would be fabulous! :)

[chrisgorgo]

What errors are you getting?

…

On Mar 21, 2017 7:07 AM, "NeuroFreakZH" ***@***.***> wrote: That would be fabulous! :) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOkp6mSxAYzM5lS3AnqPemNRX17koSLks5rn9mHgaJpZM4JxxtH> .

[NeuroFreakZH]

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]

...and slice timing info is missing.

[chrisgorgo]

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" ***@***.***> wrote: ...and slice timing info is missing. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOkp-CV0qrAM6oCU7qWU8O7ufeqOf_nks5rn-SMgaJpZM4JxxtH> .

[NeuroFreakZH]

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]

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" ***@***.***> 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 <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOkp4dGo1Sr899QrSKHt3-2MRHJc-mdks5rn_CegaJpZM4JxxtH> .

[wanderine]

And maybe you can guide me to do that ;-) 2017-03-21 16:56 GMT+01:00 Chris Filo Gorgolewski <[email protected]> :

…

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" ***@***.***> 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 > <#25 (comment) >, > or mute the thread > <https://github.com/notifications/unsubscribe- auth/AAOkp4dGo1Sr899QrSKHt3-2MRHJc-mdks5rn_CegaJpZM4JxxtH> > . > — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEGryAu2xvW4rsdniBc_qzoTDPjGGtkhks5rn_MTgaJpZM4JxxtH> .

-- Anders Eklund, PhD

[chrisgorgo]

bids-apps/BROCCOLI#8

[wanderine]

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 <[email protected]>:

…

And maybe you can guide me to do that ;-) 2017-03-21 16:56 GMT+01:00 Chris Filo Gorgolewski < ***@***.***>: > 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" ***@***.***> 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 > > <#25 (comment) > >, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/ > AAOkp4dGo1Sr899QrSKHt3-2MRHJc-mdks5rn_CegaJpZM4JxxtH> > > > . > > > > — > You are receiving this because you modified the open/close state. > Reply to this email directly, view it on GitHub > <#25 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AEGryAu2xvW4rsdniBc_qzoTDPjGGtkhks5rn_MTgaJpZM4JxxtH> > . > -- Anders Eklund, PhD

-- Anders Eklund, PhD

[NeuroFreakZH]

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

…

________________________________ Von: Anders Eklund <[email protected]> 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 <[email protected]>:

And maybe you can guide me to do that ;-) 2017-03-21 16:56 GMT+01:00 Chris Filo Gorgolewski < ***@***.***>: > 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" ***@***.***> 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 > > <#25 (comment) > >, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/ > AAOkp4dGo1Sr899QrSKHt3-2MRHJc-mdks5rn_CegaJpZM4JxxtH> > > > . > > > > - > You are receiving this because you modified the open/close state. > Reply to this email directly, view it on GitHub > <#25 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AEGryAu2xvW4rsdniBc_qzoTDPjGGtkhks5rn_MTgaJpZM4JxxtH> > . > -- Anders Eklund, PhD

-- Anders Eklund, PhD - You are receiving this because you commented. Reply to this email directly, view it on GitHub<#25 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AZQapAqroa7ACsnhntHsV8e2IgCbwWHSks5ropEUgaJpZM4JxxtH>.