Using FIJI, I am trying to save my time series in nrrd format, which will then be used in elastix for registration. While saving images manually in nrrd format works perfectly fine, it does not work in the little macro I wrote. Specifically, I have trouble in the following command,
run("Nrrd ...", "save="+target_dir+"/"+saveFileName+".nrrd");
In the macro commands site, I see that under saveas there is no option for nrrd. Is there a work around?
Thanks a lot for the help