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 <fis...@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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