Dear developers,

I've been trying to use the distribution code that you provided.

I'm running the script from my windows machine in VScode with python 3.9 and created a specific conda environment with necessary libraries (had to import the move function from the shutil library in addition).

Going through the registration step using Elastix, an error occurs in with the following command :

hu_a2s.registration(params=params_affine, result_name=file_a2s_affine, datatype='uint8')

the error being :

FileNotFoundError: [Errno 2] No such file or directory: './elastix_folder/workingDir/TransformParameters.0.txt'

Indeed the TransformParameters.0.txt is not being created and therefore raises an error when called in the following function :

move(self.elastix_path + r'/workingDir/TransformParameters.0.txt', os.path.join(self.result_path,result_name + r'.txt'))

The same goes for the expected result.0.nii.gz file in the command

move(self.elastix_path + r'/workingDir/result.0.nii.gz', os.path.join(self.result_path,result_name + r'.nii.gz'))

Could you provide some insight on how to create those files maybe modifying the affine_mouse_atlas_v6.1.txt file.

I can provide the log file from the registration here : https://filesender.switch.ch/filesender2/?s=download&token=23f95857-542a-4387-a57f-f4b987e7cfc7

the workingDir contains the following files :

Appreciate your help !