Re: [Freesurfer] question about reslicing

Does this wiki page help? http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

On 07/25/2016 04:22 PM, 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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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
    <fischl@nmr.mgh.harvard.edu <mailto: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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