Hi Thomas,

Fiji / ImageJ is probably the best way to go for converting confocal
images. You can use either nifti (nii) or nrrd format. I personally
would recommend nrrd format - I like the human readable header.

You must make sure that your images include calibration information.
They may well loose this if you are opening generic tif files with
ImageJ. You are better off using ImageJ to open your manufacturer's
confocal image format directly (eg leica lei/tif or zeiss lsm) without
trying to export from the confocal software as tif. Fiji comes with
appropriate plugins to read most proprietary confocal formats. There
are also plenty of ImageJ batch conversion macros available that you can
modify to convert a directory of eg lsm files to nrrd.

The warning that you have seen is harmless - it means that your nrrd
files do not include a definition of an anatomically-based coordinate
system (which hasn't yet been standardised for fruit flies anyway!).

As for why you are not getting any output, I'm not entirely sure, but
you should check that you can reopen your images with Fiji and that they
have sensible properties (eg voxel size).

Finally, if you want to find out more about parameters that we have used
for confocal images, see:

http://flybrain.mrc-lmb.cam.ac.uk/dokuwi...

and especially:

http://flybrain.mrc-lmb.cam.ac.uk/dokuwi...

Best wishes from Cambridge,

Greg Jefferis

PS If you are going to work with nrrd format images and are comfortable
with the command line, I also recommend installing the "unu" tool
available as part of the teem project (google: teem unu)