Hi all,
I used to use FSL3.3 version of TBSS (successfully) on my centos4 linux
box. This past Tues I downloaded & installed fsl-4.0.2-centos4_32.tar.gz.
I must be doing something seriously wrong, since every attempt at making
it through tbss_2_reg results in a super-smooth output file (as if a 100mm
smoothing kernel was passed over the entire trio of volumes in the
tbss_2_reg output file). I've tried data DTI from three different Siemens
machines (1.5 Sonata, 3.0 Trio, 3.0 Tim Trio), all with the same result. I
didn't see anything in the archives, but I'm hoping this is just a "duh" on
my part. The command sequence below, using all defaults except for bet -f,
reproduces the problem:
> cd dicom_datadir
> mri_convert 610000-8-1.dcm c8_dti.nii # raw dicom data --> nii
> eddy_correct c8_dti.nii c8_dti_eddy.nii 0 # no probs, 10 B0, 60 angles
> bet vol0000.nii.gz c8_nodif_brain -f 0.2 -m # gives a rounded frontal lobe
> dtifit -k c8_dti_eddy -o c8 -m c8_nodif_brain_mask -r bvecs -b bvals
[output from dtifit looks fine, FA included]
# re-orient our Siemens data to match the FMRIB58_FA template
> fslswapdim c8_FA x -y z c8_FA_swap
> fslorient -forceradiological c8_FA_swap
# set up filesystem
> mkdir tbss
> mv c8_FA_swap.nii.gz tbss/
> cd tbss/
> fslstats c8_FA_swap.nii.gz -R
[output = 0 1.2247] ... so use scaling of 10000
> tbss_1_preproc -f 10000 c8_FA_swap.nii.gz
> tbss_2_reg -T
The output of the last command, c8_FA_swap_FAi_to_target_nonlinear.nii.gz,
is hyper-smooth (doesn't look like an FA image at all). It's also 73Mb,
which seems rather larger than the template (at 14Mb). If create the affine
transofrm volume using ...
${FSLDIR}/bin/DR/transformation c8_FA_swap_FAi.hdr c8_FA_sw_FAi_affine.hdr \
-dofin c8_FA_swap_FAi_to_target_affine.dof -target target.hdr
the affine-reg result nicely co-registers with the FMRIB58_FA template, so
it's not tbss_2_reg, tbss_reg, or areg ... pretty much leaving nreg to
blame. If I use the affine-aligned output as the source volume for
registration, as in "tbss_reg c8_FA_sw_affine.nii.gz target" I get the same
hyper-smooth output after the nreg step.
What am I missing?
-best
Gary
