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Create default anonymisation for spectroscopy data #511

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mxochicale opened this issue Oct 8, 2024 · 1 comment · Fixed by #513
Closed
3 of 4 tasks

Create default anonymisation for spectroscopy data #511

mxochicale opened this issue Oct 8, 2024 · 1 comment · Fixed by #513

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@mxochicale
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mxochicale commented Oct 8, 2024 •
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  • Discuss with James Moggridge and Matthew Grech Sollars on what they have done for de-identification,
  • Add the spectroscopy specific ones to a new tag-operations config file,
  • Run through and share de-id files with them, to see if they are still usable.

Pre-requisites:

  • JM to share data to PIXL team

Notes:
@p-j-smith
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@p-j-smith and @mxochicale met with James Moggridge for further info on adding support for spectroscopy data:

  • Will the scanners also be producing .rda or .ima files and should we be planning to support these?

    • .ima files are legacy files produced by Siemans scanners. The scanners scanners in Grays Inn Road will produce .dcm files instead, so .ima files can be ignored. The plan is to export the DICOM from the scanners and upload to PACS, then PIXL can pull from there.
    • .rda files may also be produced by the scanners and it would be good to support these. Ideally the .rda files will be handled in the same way as raw data (uploading to shared storage on the network and have PIXL pull it from there). We also need to think about where .rda files will be sent (assuming XNAT doesn't support them), and how to link images send to XNAT with ``.rda files stored elsewhere

  • the sample data James has shared is phantom data. However, it may contain operator data that will need anonymising before using in PIXL unit tests. Alternatively, there is anonymised sample spectroscopy data available from a researcher (Chris Roden?). The researcher also has sample data for various scanners (Siemans, Phillips, ...) which may be useful in the future

  • once we have passed the data through the anonymisation pipeline, James will check that he can still run his analysis on it

  • all tags specific to spectroscopy can probably be kept, although we need to check the private tags added by Siemans in case these contain PII

mxochicale added a commit that referenced this issue Oct 15, 2024
@mxochicale
Adds configs files for mr spectroscopy with relevant tags #511
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@mxochicale mxochicale mentioned this issue Oct 15, 2024
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p-j-smith added a commit that referenced this issue Dec 11, 2024
@mxochicale @stefpiatek @p-j-smith
511 - anonymisation for spectroscopy data (#513)
3678f3c 
* Adds configs files for mr spectroscopy with relevant tags #511

* Adds Stef`s suggestion on expecting none in dicom at projects/configs/mr-spectroscopy.yaml

Co-authored-by: Stef Piatek <[email protected]>

* adds tags for 0002 and 0008 groups from `DICOM/csi_slaser_40_20_MR/1.dcm`

* adds some ~20% of the tags from `dicom.dcmread(DICOM/csi_slaser_40_20_MR/1.dcm` which might be or not included (also needs to be formated). Do we need to include all tags with a config format?

* remove ms-pinpoint from base tag operations for mr-spectroscopy

* Keep all tags unique to mr spectroscopy

We're not yet keeping nested tags except for those that cause validation errors

* Add manufacturer overrides for mr-spectroscopy

* Rename mr-spectroscopy project to test-mr-spectroscopy project

* Use latest version of dicom-validator

We're running into this issue in 0.6.3:
pydicom/dicom-validator#123

* remove manufacturer overrides for mr-spectroscopy

* remove patient id from spectroscopy anonymisation config

* Move config Acquisition DateTime, Content Date, and Content Time to mri.yaml

Also replace the tags rather than keep

---------

Co-authored-by: Stef Piatek <[email protected]>
Co-authored-by: Paul Smith <[email protected]>
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511 - anonymisation for spectroscopy data SAFEHR-data/PIXL
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@mxochicale @p-j-smith