The rawavg.mgz should be the same dimension as your T1 MPRAGE. Why are they not? Look at the dims for the volume subject/mri/orig/001.mgz
On 4/4/2022 2:25 AM, Aleksandra Szum-Jakubowska wrote:
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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
UMB_MUB
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