New to BIDS (dcm2bids config json)

[Alex Dufford]

Hi all,

I am very new to BIDS and I am trying to use dcm2bids (https://github.com/cbedetti/Dcm2Bids) to convert my data that was acquired on a Tim Trio. I am unclear on how to set up the configuration file based upon the example given. Has anyone who has used this converter and Trio data and willing to lend me a hand? Thanks so much!

Best,

Alex

[Chris Gorgolewski]

Hi,

Welcome! I personally do not have experience with this converted (I have used heudiconv before), but Christophe Bedetti is on this mailing list so hopefully he can help.

Best,

Chris

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[PERNET Cyril]

from the PRISMA, choosing the option for BIDS generates a json file that contains the relevant information -  so you don't have to do it. That's pretty much it.

cyril

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Dr Cyril Pernet,
Senior Academic Fellow, Neuroimaging Sciences
Software Sustainability Institute Fellow 

The University of Edinburgh
Centre for Clinical Brain Sciences (CCBS)
Chancellor's Building, Room GU426D
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cyril....@ed.ac.uk
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From: bids-di...@googlegroups.com <bids-di...@googlegroups.com> on behalf of Chris Gorgolewski <krzysztof....@gmail.com>
Sent: 20 July 2017 21:49
To: bids-discussion
Subject: Re: [bids-discussion] New to BIDS (dcm2bids config json)

 

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[PERNET Cyril]

@Chris Gorgolewski FYI, attached are the json files generated automatically for MPRAGE and fMRI BOLD

--

Dr Cyril Pernet,
Senior Academic Fellow, Neuroimaging Sciences
Software Sustainability Institute Fellow 

The University of Edinburgh
Centre for Clinical Brain Sciences (CCBS)
Chancellor's Building, Room GU426D
49 Little France Crescent
Edinburgh EH16 4SB
cyril....@ed.ac.uk
http://www.sbirc.ed.ac.uk/cyril
http://www.ed.ac.uk/edinburgh-imaging

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From: bids-di...@googlegroups.com <bids-di...@googlegroups.com> on behalf of Chris Gorgolewski <krzysztof....@gmail.com>
Sent: 20 July 2017 21:49
To: bids-discussion
Subject: Re: [bids-discussion] New to BIDS (dcm2bids config json)

 

To unsubscribe from this group and stop receiving emails from it, send an email to bids-discussi...@googlegroups.com.
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[Alex Dufford]

Dear Dr. Pernet,

Thanks so much for your response. I got to the point where I have the json specific for my mprage (attached). However, when I run dcm2bids ( dcm2bids -d sub1 -p 001 -c sub1_mprage_5e_20140427134518_13.json) I get the following error:

Traceback (most recent call last):
  File "/usr/local/dcm2bids/07.19.2017/scripts/dcm2bids", line 61, in <module>
    sys.exit(main())
  File "/usr/local/dcm2bids/07.19.2017/scripts/dcm2bids", line 57, in main
    return app.run()
  File "/usr/local/dcm2bids/07.19.2017/dcm2bids/dcm2bids.py", line 35, in run
    parser = Sidecarparser(dcm2niix.sidecars, self.config["descriptions"])
KeyError: 'descriptions'

Thanks for any help you can give with this error.

Best,
Alex

On Friday, July 21, 2017 at 1:46:42 AM UTC-6, PERNET Cyril wrote:

...@Chris Gorgolewski FYI, attached are the json files generated automatically for MPRAGE and fMRI BOLD

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[anandh...@gmail.com]

hi,

did you get any reply?

[Johan Carlin]

If you would consider using my fork of dcmbids, there is a tutorial demo for this here:

https://github.com/jooh/notebook_bids_OSD2018

The full config that the tutorial uses is also here:

https://github.com/jooh/Dcm2Bids/blob/master/example/bids_test5-20170120_config.json

It's for a Prisma rather than Trio but should be similar enough to get you started.

Johan