hina-shah / slicerbatchanonymize Goto Github PK

This will try to read all files in a directory as dicom files, and anonymize them accordingly.
Need to add a few more output formats.

Should be able to read files in a series format (i.e. one file per slice), and export to a format.

Creating this as a separate issue because it seems like this might take more time in early investigation.

• Exporting a Scalar volume directly into dicom format is not supported in Slicer.
• Tried going down the DICOM library path, but it's not clear if this is possible
• Looks like going through pydicom might work:
  -- When exporting a series of dicom files as a single dicom image we can read metadata from the first file, and get pixel spacing from the import dicom volume using this piece of code
  -- Need to investigate what is the correct dicom metadata for a volume image.

• Given an option to create patient IDs
• Assign anonymized Patient IDs
• Add these to the crosswalk table
• Create a mapping table for Patients as well.

Hello!
I have a folder with CBCT in dcm format.
While I am performing the Anonymization the process stops after recognizing all CBCTs, see image attached.
Is there any particular format that I need to use for the name of the files? At the moment the dcm files are named as 0001.dcm

I did not find it extension in Slicer Extension center.
Is there any other way to use this tool in Slicer?

Not sure if this would be helpful. But if the output folder has an already created crosswalk file, we can load it to not redo deanonymization. The prefix pattern can be identified with a few files, and loaded in the GUI.

The tool should be able to export to .gpil, .nrrd, .nii.gz

Need to do operations like

• Make sure that the slicer database is open, and valid
• If not open, create a new slicer database
• Make sure that the DICOM plugin is installed. If not installed - throw an error
• Close the dicom database in the end.

Not sure if these operations are necessary with the default dicom database in Slicer. These operations might be necessary when using a temporary database, or when creating a new database somewhere else (for example in the output directory).

• This could be a progress bar below or above the Start button
• Will need to add a cancel button, and handle an abort operation