dcm2bids

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Pierre Bellec

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May 3, 2017, 11:14:23 AM5/3/17
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Dear all,

At our local brain imaging centre (UNF), we are working towards shipping data prepared in BIDS to our users, in addition to the raw dicom. We have developed some bids-inspired conventions to name the sequences of each protocol, in order to facilitate the conversion. You will find the "cheat sheet" and examples here:
Feel free to comment in the document. Please be aware this is an early iteration. 

In addition, a research associate at UNF developed a handy, configurable script to convert from dicom to bids: 

Now, I am aware that other similar efforts exist, e.g.: 
Please let me know if you know of others, so hopefully we can try them out and converge on a single robust approach. 

Best,

Pierre Bellec

Satrajit Ghosh

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May 3, 2017, 11:26:44 AM5/3/17
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Cameron Craddock

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May 3, 2017, 11:32:29 AM5/3/17
to bids-di...@googlegroups.com, Yaroslav O. Halchenko

Hey Pierre,

 

Great initiative! I think that Yarek has been working on something like this too.

 

Cheers,

Cameron

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Chris Gorgolewski

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May 3, 2017, 11:34:36 AM5/3/17
to bids-discussion, Yaroslav O. Halchenko

On Wed, May 3, 2017 at 8:32 AM, Cameron Craddock <Cameron....@childmind.org> wrote:

Hey Pierre,

 

Great initiative! I think that Yarek has been working on something like this too.

 

Cheers,

Cameron

 

From: <bids-discussion@googlegroups.com> on behalf of Pierre Bellec <pierre...@gmail.com>
Reply-To: "bids-discussion@googlegroups.com" <bids-discussion@googlegroups.com>
Date: Wednesday, May 3, 2017 at 11:14 AM
To: bids-discussion <bids-discussion@googlegroups.com>
Subject: [bids-discussion] dcm2bids

 

Dear all,

 

At our local brain imaging centre (UNF), we are working towards shipping data prepared in BIDS to our users, in addition to the raw dicom. We have developed some bids-inspired conventions to name the sequences of each protocol, in order to facilitate the conversion. You will find the "cheat sheet" and examples here:

Feel free to comment in the document. Please be aware this is an early iteration. 

 

In addition, a research associate at UNF developed a handy, configurable script to convert from dicom to bids: 

 

Now, I am aware that other similar efforts exist, e.g.: 

Please let me know if you know of others, so hopefully we can try them out and converge on a single robust approach. 

 

Best,

 

Pierre Bellec

 

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yarikoptic

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May 3, 2017, 3:09:57 PM5/3/17
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We are converging! ;)
And here you can see our cheatsheet: https://docs.google.com/document/d/1EivqiAnbTGPRjav3eOsmqbOMJR5phdLrto5gFNBFpdE/edit?usp=sharing
and code is in everlasting WiP PR: https://github.com/nipy/heudiconv/pull/32

Pierre Bellec

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May 6, 2017, 1:48:47 PM5/6/17
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Thanks a lot for all the info! 

Pierre

Pierre Bellec 
Assistant professor ("adjoint sous octroi"), Department of computer science and operational research (DIRO)
Member, Centre de recherche de l'institut Universitaire de gériatrie de Montréal (CRIUGM)
Université de Montréal, Montréal, Canada
Full coordinates on my home page

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Hauke Bartsch

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May 6, 2017, 4:25:52 PM5/6/17
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Here is what we are using now in ABCD:


 Hauke

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Mahmoud Zeydabadinezhad

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Sep 11, 2017, 12:16:21 PM9/11/17
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Hi Pierre,

Is there any example or document I can refer to for using the dcm2bids and configuring my own config.json file? I looked at the github but the USAGE is not clear to me.

Thank you!
Mahmoud
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