dcm2niix customisation

installation of other versions

The “convert_to_BIDS()” function automatically uses the tested “v1.0.20211006” of dcm2niix. Other versions can be installed by changing the version number and running the script before running “convert_to_BIDS()” the first time.

Otherwise, go to your output folder, delete the dcm2niix files in it, and run the “install_dcm2niix()” version with your version number.

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

install_dcm2niix("v1.0.20181125") # if you want to install the specific version v1.0.20181125

using other arguments

You can edit the dcm2niix_argument_string in the “user_settings.R” file according to your needs.

Just read here or inspect the possible arguments from this image:

dcm2niix_argument_string <- -ba y -f %d -z y -w 0 -i y

Argument	Setting	Behaviour
-ba	y (yes)	bids anonymisation of JSON sidecar
-f	%d	string for the filename (do not change this one)
-z	y (yes)	compress the output (nii.gz instead of nii)
-w	0	in case of duplicate filename -> skip
-i	y (yes)	ignore derived, localizer and 2d images

Used arguments for conversion

Please edit these, if the conversion went wrong.