Docs for site-wide BIDS map and nrg_pipeline_dicomtobids repository

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tom.g...@gmail.com

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Sep 20, 2020, 9:28:51 PM9/20/20
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Hi,

I am attempting to use the xnat/dcm2bids-session container on a session but it is failing to find the required "site-wide BIDS map". I went looking for the docs describing this mapping but haven't been able to find them.

I then tried to track down the source code in the nrg_pipeline_dicomtobids repository but the bitbucket link appears to be broken. Has this repo been moved or is it not public?

Cheers,

Tom

Wallace, Lauren

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Sep 22, 2020, 5:05:40 PM9/22/20
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Tom,

 

Briefly, XNAT BIDS support is in two parts, an XNAT pipeline that uses dcm2niix to generate the NIFTI and sidecar, labels them according to a user-defined mapping between series description and BIDS type (this is the BIDS map mentioned), and uploads the results to two directories at the scan level (NIFTI for the images and BIDS for the BIDS sidecar), and a downloader component that is a simple REST API that aggregates the output of the pipeline into a ZIP file of a BIDS dataset for a single session using rules in a separate user-defined mapping between DICOM series descriptions and BIDS output directories (anat, func, dwi, etc). The downloader plugin (here) is functional but bare-bones as the project that our BIDS components were written to support, the OASIS study, ended up using a script-based download instead that uses standard XNAT APIs and then sorts the data into BIDS directories after the fact, which was more efficient for the volume of data and allowed (and possibly more in the BIDS idiom where a BIDS data set is more equivalent to an XNAT project than a single XNAT session)—scripts for that are here.

 

I’ve attached simple rules for both the converter and downloader, both of them use the configuration API:

 

The configuration file for the converter goes to the config API here:

 

curl -X PUT -i -k -u username https://xnat.url.here/REST/config/bids/bidsmap?inbody=true -d @conversion-sample.json

 

and the configuration file for the downloader goes here:

 

curl -X PUT -i -k -u username https://xnat.url.here/REST/projects/LaurenTest/config/downloader/default?inbody=true -d @downloader-sample.json

 

I’m afraid I don’t know where the best current location for the nrg_pipeline repos is in Bitbucket, maybe someone else on the XNAT team could chime in on that?

 

Thanks,

 

Lauren

 

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> On Behalf Of tom.g...@gmail.com
Sent: Sunday, September 20, 2020 8:29 PM
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Subject: [XNAT Discussion] Docs for site-wide BIDS map and nrg_pipeline_dicomtobids repository

 

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conversion-sample.json
downloader-sample.json

tom.g...@gmail.com

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Sep 22, 2020, 10:03:40 PM9/22/20
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Thanks for the detailed instructions Lauren!

So just to double check, the BIDS map is site-wide and the downloader configuration is project-specific?

tom.g...@gmail.com

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Sep 22, 2020, 10:31:18 PM9/22/20
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On the BIDS mapping, can it handle the case where you have multiple scans in a session that have the same series description, e.g. multiple fMRI runs?

On Wednesday, 23 September 2020 at 07:05:40 UTC+10 Lauren Wallace wrote:
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