Workshop day 2

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Altering image files

Image anonymization

Use the anonymisation function of Synedra to anonymise a DICOM series. Compare an anonymised image with the original file using LONI Inspector.

Perform another anonymisation of the same series with DICOM Cleaner. Use LONI Inspector to compare the same image of the series between this anonymisation and the original file, and between this anonymisation and that performed by Synedra.

Image conversion

Use RadiAnt to load a DICOM series and then save a slice of the series as a JPG image. This is useful for including in a publication. Note that the exported image will be rendered according to the current image settings (windows width and level, lookup table) and annotations.

Use Mango to load a DICOM series and save it as NIFTI, using the default settings (16 bit unsigned integer, little endian, .nii.gz format). Also examine the options available within the tabs of the Save As dialog - Type, Reslice, Transform, Misc.

Repeat the conversion from DICOM to NIFTI using MRIConvert, and save the resulting NIFTI file(s). Use LONI Inspector to load both NIFTI files, and use its Compare function to highlight differences between the files. You will notice that while the exported files are essentially the same, there will be small rounding differences in floating point values, and some minor fields may be used differently between the two conversion programs. The Description fields are often used differently and may be completely different between the conversion programs.

Perform the same DICOM to NIFTI conversion using dcm2niix (part of MRICroGL. Load the resulting NIFTI image into LONI Inspector and compare against the other two conversions.

Download the DICOM and ECAT versions of a PETimage volume from the I Do Imaging sample data page. Load both volumes into VINCI and use its Image Volume Arithmetic tool to compare the voxel values. You'll see small rounding differences between the two volumes resulting from the conversion.

Install MRIConvert and use it to convert a series of DICOM files to Analyze format. Then view the Analyze header contents with LONI Inspector

Editing DICOM file headers

Install DICOM Browser and use it to edit the headers of a series of DICOM files. Note which header elements are common to all files, and which differ. Do the same for two series, and note which additional fields now have multiple values.

Sending to a PACS

Send the DICOM series you just edited to a PACS server. Query the PACS to ensure the series you sent is present.