hi all,

when a .img extension file is passed to freesurfer routines, it is read in as analyze even if the header says it's a nifti image. we have observed that this causes a left-right flip in some cases. since a .img cannot exist without a header to be meaningful, shouldn't the appropriate type be detected from the header?

also it would be good to know if this behavior is consistent across all of freesurfer or restricted to certain binaries.

see below for mri_info output

cheers,

satra

$ mri_info con_0001.img
Volume information for con_0001.img
          type: analyze4d
    dimensions: 79 x 95 x 68
   voxel sizes: 2.0000, 2.0000, 2.0000
          type: FLOAT (3)
           fov: 79.000
           dof: 0
        xstart: -39.5, xend: 39.5
        ystart: -47.5, yend: 47.5
        zstart: -34.0, zend: 34.0
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r = -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =    -1.0000
              : x_a =   0.0000, y_a =   1.0000, z_a =   0.0000, c_a =   -17.0000
              : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =    18.0000
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
               -2.0000   0.0000   0.0000    78.0000
                0.0000   2.0000   0.0000 -112.0000
                0.0000   0.0000   2.0000   -50.0000
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -8

ras to voxel transform:
               -0.5000   0.0000   0.0000    39.0000
               -0.0000   0.5000 -0.0000    56.0000
               -0.0000 -0.0000   0.5000    25.0000
                0.0000   0.0000   0.0000     1.0000

$ mri_info con_0001.hdr
Volume information for con_0001.hdr
          type: nifti1
    dimensions: 79 x 95 x 68
   voxel sizes: 2.0000, 2.0000, 2.0000
          type: FLOAT (3)
           fov: 79.000
           dof: 0
        xstart: -39.5, xend: 39.5
        ystart: -47.5, yend: 47.5
        zstart: -34.0, zend: 34.0
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r = -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =    -1.0000
              : x_a =   0.0000, y_a =   1.0000, z_a =   0.0000, c_a =   -17.0000
              : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =    18.0000
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
               -2.0000   0.0000   0.0000    78.0000
                0.0000   2.0000   0.0000 -112.0000
                0.0000   0.0000   2.0000   -50.0000
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -8

ras to voxel transform:
               -0.5000   0.0000   0.0000    39.0000
               -0.0000   0.5000 -0.0000    56.0000
               -0.0000 -0.0000   0.5000    25.0000
                0.0000   0.0000   0.0000     1.0000