Hello,
We have done an MRI acquisition of an animal brain using three times the same T1 sequence. However, we are now trying to average these three data sets and do a 3D reconstruction. This is our first time doing this, so we don't know how to proceed.
For now, we have downloaded FSL and transformed our files to .nii.
Could someone help us figure out the next steps using FSL?
Thank you
Hi,
To calculate an average, first you need to make sure that the images are well-aligned and the subject/specimen has not moved between acquisitions, thus you may want to co-register your images (one option would be FSL flirt https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide).
For calculating the mean you could also make use of FSL functions, see e.g. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils (most interesting for you are probably fslmaths and fslmeants)
BR
Peter