External Email - Use Caution
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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Administratorem Panstwa danych osobowych jest Uniwersytet Medyczny w Bialymstoku. Informacja dotyczaca zasad przetwarzania Panstwa danych dostepna jest pod adresem: https://secure-web.cisco.com/1G7fVk0yj2NQ8lWF3RpIcAXswlnvuIC6QkNdtflc_gKuCwV...
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:
External Email - Use Caution
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
Niniejsza wiadomosc oraz jej zalaczniki moga zawierac informacje chronione prawem. Jesli Panstwo nie jestescie adresatem tej wiadomosci, prosimy poinformowac o tym fakcie nadawce i usunac ja wraz z zalacznikami. Kopiowanie i/lub przesylanie dalej informacji zawartych w tej wiadomosci przez osoby do tego nieuprawnione jest zabronione.
The information in this e-mail may be legally privileged. It is intended solely for the addressee. Access to this e-mail by anyone else is unauthorised. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is prohibited and may be unlawful.
Administratorem Panstwa danych osobowych jest Uniwersytet Medyczny w Bialymstoku. Informacja dotyczaca zasad przetwarzania Panstwa danych dostepna jest pod adresem: https://www.umb.edu.pl/rodo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Aleksandra Szum-Jakubowska -
Douglas N. Greve