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
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: [XNAT Discussion] Docs for site-wide BIDS map and nrg_pipeline_dicomtobids repository
* External Email - Caution * |
--
You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
xnat_discussi...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/xnat_discussion/4c63b321-94bf-47e1-a641-9ba7ae8392ean%40googlegroups.com.
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.