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

Unfortunately I don’t use windows. My first thought is either a problem with the Windows binary (Torsten always recommended Cygwin rather than pure Windows). Another possibility is a memory issue during the reformatting. Have you considered using Cygwin or WSL as recommended in the same thread?

On windows you can run the linux version now fairly easily with the updated WSL, I have a Fiji GUI using that method, you can see if thats fits your needs.


https://github.com/sandorbx/Paralell-Fij...

Thanks, Sandor. I'd second that using WSL is now a good option and encourage people to try his Fiji GUI.
Originally posted by Sandor Kovacs: