Hello,
I have been trying to register 3D stacks of whole brains. 

The MacOS implementation did not give any problem, but I wanted to use my desktop computer running Windows 10 as it has a 24-Core Processor. I have followed the CMTK instructions from Gabriella Sterne (https://www.nitrc.org/forum/message.php?...) and I was able to run the registration. However I am only able to do so when I set the number of CPU cores to use to 4:

cd "C:\CMTKregistration"
"C:\Strawberry\perl\bin\perl" "C:\CMTK\bin\munger" -b "C:\CMTK\bin" -a -w -r 01 -X 52 -C 8 -G 80 -R 3 -A "--accuracy 0.4" -W "--accuracy 3.4" -T 4 -s "C:\CMTKregistration\template\template.nrrd" "images"

If I set it to more than 4, say 12: 

cd "C:\CMTKregistration"
"C:\Strawberry\perl\bin\perl" "C:\CMTK\bin\munger" -b "C:\CMTK\bin" -a -w -r 01 -X 52 -C 8 -G 80 -R 3 -A "--accuracy 0.4" -W "--accuracy 3.4" -T 12 -s "C:\CMTKregistration\template\template.nrrd" "images"

the registration fails at the reformat step and does not produce a "reformatted" folder. 
I attach my registration folder as an example. The images are very downsampled. 

Many thanks in advance for any hints,
Claudio