I use the ImageJ as my default image viewer program. In order to view .nii format images, I installed the Nifti_io plugin following the instructions in here!
However, when I try to open an image from terminal, it just says
File is not in a supported format, a reader plugin si not available, or it was not found. /tmp/TempFile-2805.nii
If I try to open the image just by clicking in ImageJ Plugins>Nifti Reader>/[imageURL] it opens it correctly, but I would like to open it directly from terminal. Thank you very much.
It looks like the Nifti_io plugin adds commands for importing but doesn't use the I/O plugin mechanism of ImageJ: HandleExtraFileTypes.
I would recommend downloading Fiji and giving it a try. It bundles a lot of useful ImageJ plugins, and the default File > Open will fall back to Bio-Formats, which provides a NiftiReader implementation.
来源：https://stackoverflow.com/questions/25865762/problems-with-an-imagej-plugin