Degibbing Images - CoBrALab/documentation GitHub Wiki

Why would you need to do this?

Sometimes the mouse images we acquire at the CIC or receive from collaborators have a distinctive pattern of ringing, known as a Gibb's Artifact or Gibb's Ringing. You can read more about it here: https://mriquestions.com/gibbs-artifact.html .

In order to help remove some of the ringing, we can use a tool from MRtrix3 (https://www.mrtrix.org/documentation/)to de-gib the image.

When to De-gib

It is considered best practice to degib before preprocessing, but we are investigating whether this is accurate or not, and will update this section with the new information.

How to De-gib.

In a terminal, create a file called degibbed (mkdir degibbed)

Then run the following code:

# at the cic, load this package
module load mrtrix3/3.0.8 

# Point the script at the images you want to degib
for file in PATH_TO_IMAGES/*nii.gz; 
#Run the script from mritrix3
        do mrdegibbs $file degibbed/$(basename $file .nii.gz).degibbed.nii.gz; 
done 

The script is very fast (several seconds per image) so you don't need to run it in parallel.