Hi all,
I'm attempting to use FreeSurfer 5.1 (version block below) to process
some older T1 scans collected on a 1.5T magnet with a native voxel size of
0.9375x0.9375x1.5mm. Overall, FreeSurfer seems to deal with these scans
just fine (resampling to 1 mm isotropic, etc.), but I'm a little concerned
about the results of the built-in image normalization.
The potential issue is illustrated in an image that I've posted to
http://imgur.com/NiEVQ. The isolated plot to the right shows the intensity
histogram that we've observed for more recent 3T T1 scans, with an obvious
WM peak at 110 and a GM peak around 65. Meanwhile, each of the six plots to
the left is the intensity histogram for one of our 1.5T scans. Although
they are internally consistent (with the upper-leftmost example being
something of an outlier), the GM peak is much closer to the WM peak, with a
mode around 85.
I'm wondering whether this reduced GM/WM separation is likely to
influence the tissue segmentation process, and if so how I might best remedy
the situation. At a guess, mri_normalize or mri_ca_normalize seem like
useful functions, but I haven't found the documentation for either to be of
much help. Any assistance or advice would be greatly appreciated! Thanks,
Dave Warren
--
Post-doctoral Fellow
Neurology Department
University of Iowa Hospitals and Clinics
davideugenewar...@gmail.com
-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
$Id: FreeSurferEnv.csh,v 1.79.2.1 2011/03/29 22:06:48 greve Exp $
FREESURFER_HOME /usr/freesurfer
FSFAST_HOME /usr/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/freesurfer/subjects
MNI_DIR /usr/freesurfer/mni
FSL_DIR /usr/fsl
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