I’m trying to get the intracranial volume of my subjects using FSL and have only been able to find a old pipeline from ENIGMA but the value it gives for intracranial volume is a decimal (0.809…) which doesn’t seem right. The pipeline determines the intracranial volume via the inverse determinant of the affine matrix used to register the T1w image to MNI space which seems outdated because it’s FLIRT based and that sort of registration should be non-linear. Does anyone know a better way to get intracranial volume using FSL?
Hello,
I’ll preface this by saying that I would go for an ICV estimate from FreeSurfer compared to FSL.
That decimal you are getting might be the fraction of that brain size relative to the template brain? If you are interested in just brain volume, then you can just run BET on your data and multiply the number of brain mask voxels by your voxel size. Again, freesurfer recon-all would probably be a better tool.
Best,
Steven