TORTOISE is a very useful tool and I'm pleased to use it to process pre-clinical data from Bruker scanners.
I have noticed however some issues with my anatomical images not matching my reoriented DWIs and I wonder if there is a good solution for this. In particular, I don't want to use a third party software (e.g. mipav or FSL) to reorient my anatomical images because I'm worried about how it will affect the header information. Is there a TORTOISE function that is similar to ReorientImage, but for non-DWI data?
Unfortunately at the moment we do not incorporate any reorient image tool for anatomical images. While we have 'ReorientImage' command for DWIs in DIFFPREP, we have relied on ANTS 'ReorientImage' command or AFNI '3dresample' command, to reorient anatomical images, as the resulting image headers are compatible with TORTOISE headers. Please let us know if you encounter issues despite using either of these commands. In the future, we intend to have a TORTOISE reorient image specific to orienting anatomical images.