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Hello, I am trying to run a VBM analysis by using the white matter and the grey matter masks from Freesurfer, because, often, other tools are not able to calculate a correct white matter and grey matter masks. When I have these masks, I have to apply them to my original T1 images. However, the original T1 is in different space. I can resample the ROIs (WM and GM) in order to apply them to my original T1, but my question is: Can I use the orig.mgz from Freesurfer as my T1 for VBM, or does it have different intensity from my real T1 acquisition?
Thanks, Maurizio
Hi Maurizio
the orig.mgz has been converted to 1 byte/pixel and 256^3 1mm isotropic. You can use mri_convert to go back to your original data space via:
mri_convert -rl orig/001.mgz <input volume> <output volume>
cheers Bruce
On Tue, 18 Dec 2018, Maurizio Bergamino wrote:
External Email - Use Caution
Hello,I am trying to run a VBM analysis by using the white matter and the grey matter masks from Freesurfer, because, often, other tools are not able to calculate a correct white matter and grey matter masks. When I have these masks, I have to apply them to my original T1 images. However, the original T1 is in different space. I can resample the ROIs (WM and GM) in order to apply them to my original T1, but my question is: Can I use the orig.mgz from Freesurfer as my T1 for VBM, or does it have different intensity from my real T1 acquisition?
Thanks, Maurizio
External Email - Use Caution
Thank you!
Il giorno mar 18 dic 2018 alle ore 11:43 Bruce Fischl < fischl@nmr.mgh.harvard.edu> ha scritto:
Hi Maurizio
the orig.mgz has been converted to 1 byte/pixel and 256^3 1mm isotropic. You can use mri_convert to go back to your original data space via:
mri_convert -rl orig/001.mgz <input volume> <output volume>
cheers Bruce
On Tue, 18 Dec 2018, Maurizio Bergamino wrote:
External Email - Use CautionHello,I am trying to run a VBM analysis by using the white matter and
the grey matter masks from
Freesurfer, because, often, other tools are not able to calculate a
correct white matter and grey matter
masks. When I have these masks, I have to apply them to my original T1 images.
However, the original T1 is in
different space. I can resample the ROIs (WM and GM) in order to apply
them to my original T1, but my
question is: Can I use the orig.mgz from Freesurfer as my T1 for VBM, or does it have
different intensity from my real
T1 acquisition?
Thanks, Maurizio
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Maurizio Bergamino