Hi, This is the command line for reslicing: mri_convert -rl aseg.mgz thalamus.nii resliceduncoregtahalmus.nii
thalamus.nii is the thalamus mask obtained by using the following command: mri_binarize --i aseg.mgz --match 10 --o thalamus.mask.nii.gz
and I have attached the out put.
Thank you!
On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dorsa
you need to give us more details. What was your reslicing command line? And the screen output?
Bruce
On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
Hi,
I re-sliced my left thalamus so that the size and number of slices correspond with the original MRI, but when I open it in freeview, it shows an extra part( like a cube) on the bottom of the image ( I have attached the mask). do you have any idea how to solve that? Also how can I make sure that the position and size of the thalamus makes sense since the thalamus mask has a different slice size and number than the original mri?
Thank you
Dorsa
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