Installing dcm2niix on Ubuntu

Find the latest release:

https://github.com/rordenlab/dcm2niix/releases

Download the dcm2niix_lnx.zip and install the latest binaries:

Reload shell or open a new terminal and run:

dcm2niix


Update: Thanks @layerfmri. If one has AFNI installed, dcm2niix_afni should do the same. However, check the changelog to not miss any critical updates.

2 thoughts on “Installing dcm2niix on Ubuntu

  1. I love dcm2niix, even isisconv is looking like choirboy next to it.
    How do you apply it? like this? dcm2niix -z y -f S_%p_%t_%s -o ../ ./

    Is dcm2niix_afni literally the same? This would mean that I don’t even need to run the four steps you describe.

    Like

    1. If you want it isisconv like, then I would call it like: dcm2niix -ba y -z y -o ${output_dir} -f S%s_%d_e%e ${input_dir} , the main difference being, the echo-time is not in the filename, its in the .json file that’s created. Regarding dcm2niix_afni, its a slightly older binary (v1.0.20181125 in AFNI version AFNI_20.0.18 ‘Galba’) than the one available in the dcm2niix Github (v1.0.20190902). Since the changelog does not reflect critical updates, so you should be okay with dcm2niix_afni.

      Like

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