Dear group,

I have a T1 dicoms that looks like that:

But the T1.mgz recon-all produces looks like that:

How can I fix this skewness?
Here is the dicoms info:

  type: MGH

  dimensions: 640 x 640 x 243

   voxel sizes: 0.390625, 0.390625, 1.000000

          type: SHORT (4)

           fov: 250.000

           dof: 1

        xstart: -125.0, xend: 125.0

        ystart: -125.0, yend: 125.0

        zstart: -121.5, zend: 121.5

            TR: 700.00 msec, TE: 15.00 msec, TI: -1.00 msec, flip angle: 120.00 degrees

       nframes: 1

       PhEncDir: ROW

       FieldStrength: 3.000000

ras xform present

    xform info: x_r =  -1.0000, y_r =  -0.0000, z_r =  -0.4231, c_r =   -55.4712

              : x_a =  -0.0000, y_a =   0.0377, z_a =   0.9059, c_a =    29.9016

              : x_s =   0.0000, y_s =  -0.9993, z_s =   0.0165, c_s =   -19.3352

talairach xfm :

Orientation   : LIA

Primary Slice Direction: coronal

voxel to ras transform:

               -0.3906  -0.0000  -0.4231   120.9404

               -0.0000   0.0147   0.9059   -84.8789

                0.0000  -0.3903   0.0165   103.5695

                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -0.138228

ras to voxel transform:

               -2.5600  -1.1949  -0.0451   212.8522

               -0.0000   0.0467  -2.5601   269.1053

                0.0000   1.1031   0.0416    89.3201

               -0.0000  -0.0000  -0.0000     1.0000

Thanks!

Noam

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