Joseph, We do have an IntraDB-side dcm2nii pipeline that we haven't yet generalized or documented for release. The source code is, however, available for it. It's an XNAT pipeline, and here is a link to the pipeline XML:
https://bitbucket.org/hcp/intradb_pipeline_customizations/src/5f553155d278feadca75bbfed47fb7a7b4f1f5cc/templates/misc/catalog/HCP/HCPDefaceDicomToNifti.xml?at=default&fileviewer=file-view-default It references XML resource descriptors found here: https://bitbucket.org/hcp/intradb_pipeline_customizations/src/5f553155d278feadca75bbfed47fb7a7b4f1f5cc/templates/misc/catalog/HCP/resources/?at=default The resource descriptors refer to script found here: https://bitbucket.org/hcp/intradb_pipeline_customizations/src/5f553155d278feadca75bbfed47fb7a7b4f1f5cc/templates/misc/catalog/HCP/resources/scripts/?at=default There's definitely some hard-coding of series description, scan type and path information that's very specific to the HCP project. Our plans are to turn this into something more generalized and distributable under the Connectome Coordination Facility. Regards, Mike ________________________________ From: [email protected] [[email protected]] on behalf of Naegele, Joseph (NIH/NIMH) [C] [[email protected]] Sent: Friday, October 30, 2015 1:13 PM To: [email protected] Subject: [HCP-Users] automated DICOM to NIFTI conversion As part of implementing the HCP Minimal Preprocessing Pipeline I'd like to programmatically convert our MR DICOM data into NIFTI files in the directory structure used in the data releases. I know how to do this from scratch using dcm2nii, but I'm assuming this step is already implemented in the HCP IntraDB. Is something like this available or should I roll my own tool that creates the directory structure, converts DICOM to NIFTI, and properly names the resulting files? — Joseph Naegele [C] FMRIF/NIMH/NIH [email protected] 301-496-8101 B10-1D80 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). 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. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
