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
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