Hi Mrtrixers,
I am trying to follow the work flow for quantitative analysis.
dwibiascorrect worked just fine. However my output folder of dwiintensitynorm contains only empty images.
Any idea why this is happening?
The command does not output any error, and FA template and FA mask are correctly created.
I d appreciate your help
Cheers
Chiara
Hi Chiara,
It’s hard to say what is going wrong without seeing your data. There are only a few steps after the creation of the FA template and WM mask. So it should be possibly to work out what is going wrong by looking at the temporary working directory, and manually running each of the commands in the script after the mrthreshold command. You can specify where the temp directory is saved using the -tempdir option. You also need to specify -nocleanup, to make sure the temp directory is not removed when the script exits.
When you say you have empty images, do you mean all voxels contain zeros? You might want to check this with mrstats.
Cheers,
Dave
Dear Dave,
thank you for your reply.
I actually just solved the issue. It was a very silly mistake in bval files containing 1000s instead of 0s.
Cheers
Chiara