Since pulling the new scripts from mrtrix last week, I not cannot run dwiintensitynorm. I have double checked and I have all of the files in the correct folders. I receive the below error after running the following command:
dwiintensitynorm DWI_mifs_n105/ DWI_masks_n105/ DWI_intensity_nomrmalised_output_n105/ Output_FA_Template_n105.nii.gz Output_FA_Template_Mask_n105.nii.gz -force
Your version of cp seems to not support recursive copy with symbolic link dereferencing. Is this OSX?
For now, it should work when you remove the -L option in the line that starts with
runCommand('cp ...' in the script (mrtrix3/scripts/dwiintensitynorm).
It would be great if you could test if
cp -L -R works for you.
Thank you once again for the speedy reply. Yes, I am running OSX. I tested cp -L -R in the terminal and it actually works fine. What is strange, however, is that if you use a lower case r it errors out. As far as I know both upper and lower case r’s both stand for recursive. It’s possible that I will only need to change the lower case r to a capital R in the script and it will work.
To follow this up, I changed the lower case -r to an upper case -R and left the -L in the script and it appears to be running correctly now.
Thanks for getting back about this! I’ll change the code accordingly.
Changes are merged. To get your mrtix3 back into a clean state, execute in the main mrtrix3 folder:
git checkout scripts/dwiintensitynorm