Hi Dorsa
did you create the aseg.mgz from 1mm data (using the standard "conform" process), or higher res? The file you sent is higher:
mri_info resliceduncoregtahalmus.nii.gz Volume information for resliceduncoregtahalmus.nii.gz type: nii dimensions: 512 x 512 x 288 voxel sizes: 0.488281, 0.488281, 0.625000 type: SHORT (4) fov: 250.000 dof: 0 xstart: -125.0, xend: 125.0 ystart: -125.0, yend: 125.0 zstart: -90.0, zend: 90.0 TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present
it also has strange values in it (-32K and 32K, so probably things that can't be represented as a short). Does your aseg.mgz look right?
cheers Bruce
On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
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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