open-discussion > Voxel based morphometry based on T2 / FLAIR scans
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Jul 11, 2023  01:07 PM | jothini
Voxel based morphometry based on T2 / FLAIR scans

Dear all, 

is there any way to extract morphometric measures (such as volume and thickness information) from a 3D T2 or 3D FLAIR scan without the corresponding 3D T1 scan? The dataset I am using only contains 3D T2, 3D FLAIR and 1D T1 images. cat12 in SPM for example only supports T1 images, so I was wondering if there are any other possibilities to do VBM with FLAIR or T2. 

Thank you,


Jul 11, 2023  03:07 PM | Marcel Daamen
RE: Voxel based morphometry based on T2 / FLAIR scans

Hello Jothini,

actually an unusual constellation. The traditional SPM-based DARTEL-VBM workflow should in theory be able to work with T2-weighted images, since the unified segmentation approach from which the tissue maps are derived is agnostic to the modality (indeed, I already performed T2 segmentations for different purposes, and was quite satisfied).

Of course, this also depends on the characteristics of your images: As far as I recall, voxels need to be isotropic (i.e., usually 1*1*1 mm) - which deems it unusable for clinical sequences which typicall have high in-plane resolution, buth thick slices. I guess for your 3D T2 and Flair this will not be the case

Otherwise, you may consider to change into the FreeSurfer universe: The new SynthSR toolbox claims to close the gap for clinical data:

Good luck,