DICOM Anonymization and NII Creation with dcm2nii

This short video describes how to use the dcm2nii program to anonymize DICOM images and convert them to NII format. The NII format is a "cleaner" format that makes it easier to store and distribute imaging studies. This video is part of a tutorial available at neurorad.link/skull as well as a UA-cam playlist at neurorad.link/skullvideos

[@anfelsarabouachat8338]

thank you for the video, it helped me alot, but i'm curious why does it generalize two nifti files? in my case i gave the software a chest CT scan folder and it returned 6 compressed nii files ? how do i know which one am i supposed to use?

[@justincramer9557]

Often it's doing some sort of correction such as for gantry tilt in the extra file. Typically it will add a prefix like "o_" to the corrected file. Check out the dcm2nii documentation to figure out what exactly it's doing. Or...you just have multiple series in a folder of DICOM files and it's creating an nii for each of them. View the nii files to find out - you can, for example, view them in 3D Slicer

[@anfelsarabouachat8338]

@@justincramer9557 bless your soul ♡ u helped me alot 😊 thank you

[@puggyk4220]

Hello. i am novice of Dicom. i want to process anonymization quickly with pyspark. how can i do that??

[@justincramer9557]

I've never used pyspark. I did tweet (@justincramer) my own python code for DICOM anonymization at github.com/radiplab/dicom_utils - comes with no guarantees whatsoever but may provide some guidance.

[@alaahdr8747]

how i open nii file

[@justincramer9557]

I'd recommend 3D Slicer. Free, works on all platforms.

[@CheeseLuver]

Where did you get this gui tool?

[@justincramer9557]

They're now recommending using the newest version, MRIcroGL: www.nitrc.org/projects/mricrogl - run mricron.exe, then go to Import --> Convert DICOM to NIfTI. The GUI tool looks a little different but is still pretty straightforward.