sorry, I'm confused about what you are trying to do. Can you start from the
beginning and explain? If the data you have is 1mm but upsampled by
the scanner there is really nothing to be gained by processing the
upsampled data and it will waste lots of time
cheers
Bruce
On Mon, 25 Jul 2016,
Dorsa Haji Ghaffari wrote:
Yes I created it using the higher resolution and I think it looks fine. I
attached the aseg.mgz. Is there any way to create the thalamus mask with the
original properties ( same as the original mri) at the first place? I need
to make sure the size and position of the thalamus corresponds to the
original mri.
Thank you!
Dorsa
On Mon, Jul 25, 2016 at 3:29 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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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