Thank you for this software!
 
I am attempting to apply a linear transformations to multiple images by scripting with the reslice command.  However when I use the reslice command in ART 2.0, it returns an error of .hdr .img not found (see below).  
 
$reslice -nn -T 026_1p5T_brainmask_to_B0 -nx 82 -ny 82 -nz 49 -dx 3 -dy 3 -dz 3 -i CCaudate.nii -o rCCaudate.nii
Applying the nearest neighbor interpolation method.
Error: cannot read CCaudate.nii.hdr
Writing rCCaudate.nii.img ...
 
It does work when I convert my niftis to analyze format, but would like to avoid this if possible.
 
Does this reslice executable that you mention in the previous post, work with nifti format?
I have tried to use the GUI by Utilities - Reslice and then File - Save as image, however the software acts like it is saving the file, and then I can not find it written file.
Thanks,
Rachael