Dear Gabriella,

A few comments.

* The two munger command lines (1, 2 below) should both result in reformatting of your image (the -f 01 switch in the second command doesn�t change anything since the default channel used for registration is channel 01)
* You can add a verbose switch (-v) to the munger command lines and this might give additional details
* You can run the reformatx command line directly from the windows cmd.exe

reformatx -o myoutput.nrrd --floating myinput.nrrd mytemplate.nrrd myregistration.list

for testing purposes.
* You can use nrrd rather than pic 16 bit images (save from Fiji)
* If it is really *recently* that the script fails (and not that these new input images are somehow different � have you tested old input images?) then it obviously suggests an external change on your system.

Hope some of this might help. Best,

Greg.