Dear Freesurfer Experts,
I conduct the segmentations' examines using Freesurfer recon-all (for segmentation hippocampus and ventricles), SAMSEG (for ventricles) and using FSL FIRST (for hippocampus). Now I have a problem with compare the result (calculating overlap).
For Freesurfer and FIRST I used T1 MRAGE image (dimentions 176x256x256).

For Samseg I used T2 FLAIR images coregistered to T1 MPRAGE (dimentions 176x256x256)
I have result from Freesurfer with dimensions 256x256x256

I have results from FSL First and SAMSEG with dimensions 176x256x256.

It is important that all results are concerned other spaces, so I cannot calculate overlap using that results and I have to perform transformation to the same space.

I tried doing this:

mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz

but my rawavg image has dimensions 176x256x174).
But when I used brain.mgz or T1.mgz image, my results are moved. I have no idea how to perform the properly inverse transformation for getting segmentation results in originally T1 MPRAGE space.

Could You give me some advice?

Thanks a lot for your help.

Best regards,
Aleksandra

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