Hi Ho-Joon

I'll cc Andre van der Kouwe who created the protocol. You generally need to match bandwidth and readout direction to match distortions. The bandwidth of the 3D FLAIR sequences if typically quite high, so for the T1 we usually go to multiple echoes like MEMPRAGE. I don't think we typically do fat-sat in the FLAIR, but I defer to Andre

cheers Bruce

On Wed, 31 Oct 2018, Lee Ho Jun wrote:

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Hello freesurfer users. I am a radiologist, who is trying to setup a protocol for freesurfer segmentation.  I came to know that with 3D T2 weighted images, or 3D FLAIR images, I can get better surface segmentations, and based on search of previous archives of the mailing list, I found that 3D FLAIR images may give better segmentations.  My question is that whether applying fat suppression will change the results, since, fat suppression tends to lead to signal dropouts in areas of high susceptibility changes, such as near mastoid air cells.

Also, I am a little confused about the bandwidth matched protocols, will "matching" the bandwidths suffice?

Best wishes,  Ho-Joon Lee.