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Hi Jin,

To me it doesn't sound like a resolution issue: samseg will happily "eat" whatever resolution you have in your images, although for multicontrast data such as yours you'd need to resample all contrasts to the image grid of one contrast (typically T1 since it's higher resolution). I'm guessing top/bottom axial slices in the FLAIR were simply not acquired?

Koen


On Mon, Oct 21, 2024 at 4:32 PM Jin Liu <jin.liu@stonybrook.edu> wrote:

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Hello Freesurfer team,

 

I tried to use SAMSEG-long to deal with my longitudinal data with paired MPRAGE and FLAIR images. But when I checked the original FLAIR images I have, I found that they have a voxel resolution of 1.333333 x 1.333333 x 2.000000. When I view it on Freeview, although the axial view is fine, only a rectangular portion of the sagittal and coronal brain is available, with the top and the bottom cut off. I guess it’s probably due to resampling issue that assumes isotropic voxels which we do not have. Is there any way to fix this problem?

 

Best,

Jin

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