Hi Christopher
try outputing nifti from FSL instead of analyze and see if that helps. Don't go through analyze at all.
cheers, Bruce
On Wed, 19 Oct 2011, Christopher McCarthy wrote:
Dear FreeSurfer Gurus,
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