Hello,

I am using CMTK 3.3 on Windows 10. I am trying to run the following registration using the reference image Ref.nrrd and the image to be registered tERK_RegTest.nrrd. I am using a bat file with the following command: "registration --initxlate --dofs 6,9 --auto-multi-levels 4 -o affine11to8.xform Ref.nrrd tERK_RegTest.nrrd"

The images are in the same folder as the bat file, so the directory is correct, but when I run this code I get the error "Could not find file Ref.nrrd".

Has anyone seen this error before? I have little experience with the Windows command line, I would very much appreciate some help on this.

Thanks very much!

Hi Josh -

Is this problem limited to that one file, or do you get the same error replacing "Ref.nrrd" with a different file name?

Also, things to try:

- use ".\Ref.nrrd" (Not sure this makes sense in Windows, but always a good thing to try on Linux)

- use full path to file, e.g., "c:\Data\My Files\Ref.nrrd"

Finally, my standard recommendation for Windows users - consider switching to the Cygwin version of CMTK, since it is more optimized than the Windows binaries. I built the latter with the free MS compilers (thus without OpenMP), resulting in very limited multi-processor support.

Best,
  Torsten

Hi Torsten,

Thanks for the prompt response.

I've tried other images of different names, same error message.

I have tried ".\Ref.nrrd" and using the full file path.

I'll try using Cygwin when I get a chance sometime next week and let you know how it goes.

Thanks for your time!

Another couple of ideas -

Try the "describe" tool like so:

describe.exe Ref.nrrd

That should rule out any issues related to the more complex sequence of command line arguments for "registration".

And see if a different image format works. For example, try a NIfTI file (.nii, or .hdr/img pair).

There is certainly a possibility that the Nrrd reader specifically is having problems.

Best,
  Torsten

I have installed CMTK 3.3 on windows as well, and I am experiencing the same error when I try to use warp.exe. It said the file does not exist. I am trying to run .nii files.

Reformatx also gives an error: 
The file/directory C:/registration/working/warp_output_transform does not exist or cannot be read

I will try install the Cygwin version.