RE: [XNAT Discussion] Re: Questions about Anonymization
Archie, Kevin
Hi, David,
I haven’t made any recent changes to the DicomBrowser internals, though I am hoping to make some improvements in the next few months (mostly to support sequences) and could address performance issues along the way. Any details you can provide would be helpful: what version of DicomBrowser you’re using, your OS and version, and where the files you’re loading are: on a local drive, removable media, NFS mount, etc.
Thanks!
- Kevin
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com]
On Behalf Of David Gutman
Sent: Monday, June 18, 2012 6:47 AM
To: xnat_di...@googlegroups.com
Subject: Re: [XNAT Discussion] Re: Questions about Anonymization
Ok-- that seems reasonable.
The only issue I've had with DicomBrowser is that loading a session (and populating the tags) can be quite slow, depending on the # of files in the DICOM session. Are there any JAVA tricks you've done to speed this up....
I'll probably pick your brain a bit more at the workshop....
On Sat, Jun 16, 2012 at 5:06 AM, Simon Doran <simon...@icr.ac.uk> wrote:
David,
Your experience is not unlike what we have encountered when uploading Phase 1 clinical trials to our XNAT system, particularly those done in the "bad old days".
Although everyone appreciated the need for anonymisation, they all went about it in different ways with, essentially, no standardisation of which DICOM tags were kept or removed. Quite often, the anonymisation was done by hand with manufacturer tools at the scanner, and before moving data to the XNAT repository, I am very careful to check for odd bits of PHI in unexpected places. Furthermore, we have quite a heterogeneous portfolio of MR scanners and the different manufacturers include different fields (even between different models from the same manufacturer). Add to this the differences when we attempt to archive the data generated in multi-centre trials, where every participating team has a different local policy for clinical data.
We spent quite a while thinking about how we manage this situation. Prospectively, things will be easier, because we are conscious of these considerations in the design of new multi-centre trials now. However, for retrospective data, we are proceeding as follows:
1. Use DicomBrowser.
2. Where whole trials have the same behaviour, set up an anonymisation script - very quick to do once you have a few examples - based on a test example of one of the files. If there are any existing data in the file (e.g., previous clinical trial patient codes) that can be used to assign an anonymised name, then put this into the script. Otherwise, assign an anonymised name via the DicomBrowser GUI.
3. Create a separate spreadsheet to record the mapping between the true name and anonymised name, print it out and physically lock it away somewhere.
4. Regardless of whether you think you know what is happening when you run the script, always look at the DICOM metadata for each patient session before and after running the DicomBrowser anonymisation script and scan for unexpected PHI.
5. Use the "Send" feature of DicomBrowser to upload the data into XNAT, having previously used the script to setup the Patient Comments tag (0010,4000) appropriately.
Although this method won't be applicable to situations with thousands of patients, I find that it only takes about two or three minutes to process a single patient session and I managed to upload around 8 entire Phase 1 clinical trials over a weekend (about 120 imaging sessions in total), so it wasn't too onerous.
Simon
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David A Gutman, M.D. Ph.D.
Assistant Professor of Biomedical Informatics
Senior Research Scientist, Center for Comprehensive Informatics
Emory University School of Medicine
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