We are looking for a way to normalize the intensity histogram for our subjects. In the past we have used Brain Image Java, using FSL-Fast inhomogeneity corrections. Unfortunately we are unable to open the output files (.img, .hdr) in FreeSurfer. When trying to import the files (after converting them to nii) we get a talaraich error:

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)

here is the mri_info for a subject we get this error with:

Volume information for S029_nii
          type: nii
    dimensions: 256 x 256 x 100
   voxel sizes: 0.9375, 0.9375, 1.5000
          type: SHORT (4)
           fov: 240.000
           dof: 0
        xstart: -120.0, xend: 120.0
        ystart: -120.0, yend: 120.0
        zstart: -75.0, zend: 75.0
            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 =     0.0000
              : x_a =   0.0000, y_a =   1.0000, z_a =   0.0000, c_a =     0.0000
              : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =     0.0000
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
               -0.9375   0.0000   0.0000   120.0000
                0.0000   0.9375   0.0000 -120.0000
                0.0000   0.0000   1.5000   -75.0000
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1.31836

ras to voxel transform:
               -1.0667   0.0000   0.0000   128.0000
               -0.0000   1.0667 -0.0000   128.0000
               -0.0000 -0.0000   0.6667    50.0000
                0.0000   0.0000   0.0000     1.0000

We are either looking to get the files we currently have to import correctly in FreeSurfer, or import our DICOM files into a program and normalize the intensity histogram and output a file freesurfer can read. We are looking to get rid of hyper intensities in the temporal and frontal lobes that cause main and pial surface errors.

Thanks for whatever help you can give, now and in the future.

Chris McCarthy