questions > DCM2NIIX convert CT scans with localiser -- no output
Jun 26, 2020  05:06 AM | Wenwen Li - University of Sheffield
DCM2NIIX convert CT scans with localiser -- no output
Hello,

I am converting brain CT scans to NIFTIs. Some of the scans has localiser slices in the DICOM folders.

I used the DCM2NIIX optiion -i y to try to only convert the slices that are not localiser. However, it didn't give me any output. I think the reason is that all the slices in this folder are derived. According to the dcm2niix doc http://manpages.ubuntu.com/manpages/focal/man1/dcm2niix.1.html

-i
Ignore derived, localizer and 2D images.

Since the first slice image type is 'DERIVED\PRIMARY\LOCALIZER\CT_SOM5 SPO' while the rest of the slices are 'DERIVED\PRIMARY\AXIAL\CT_SOM5 SPO', i.e., all the slices are derived, I cannot get any output if I set -i y.

May I ask if there is any other way to convert the scan which has all derived slices, but not convert the locaiser slice to the final NIFTI?

Many thanks,
Wenwen

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TitleAuthorDate
DCM2NIIX convert CT scans with localiser -- no output
Wenwen Li Jun 26, 2020
Chris Rorden Jun 26, 2020
Wenwen Li Jun 26, 2020