Hi,
Given that brain extraction and segmentation (BET and FAST) seem to
have worked fine on your data, it's surprising that the linear
registration is failing - this is unusual for the FSLVBM scripts. You
hopefully can resolve this by:
cp /usr/local/fsl/bin/fslvbm_2_template .
then edit this script and change the lines
echo "${FSLDIR}/bin/fsl_reg ${g}_GM $T ${g}_GM_to_T -a" >> fslvbm2b
echo "${FSLDIR}/bin/fsl_reg ${g}_GM $T ${g}_GM_to_T_init $REG -
fnirt \"--config=GM_2_MNI152GM_2mm.cnf\"" >> fslvbm2d
to
echo "${FSLDIR}/bin/fsl_reg ${g}_GM $T ${g}_GM_to_T -a -flirt \"-
nosearch\"" >> fslvbm2b
echo "${FSLDIR}/bin/fsl_reg ${g}_GM $T ${g}_GM_to_T_init $REG -
flirt \"-nosearch\" -fnirt \"--config=GM_2_MNI152GM_2mm.cnf\"" >>
fslvbm2d
This turns off the full rotational search in FLIRT but will rely on
all your data having the same initial general orientation as
/usr/local/fsl/data/standard/MNI152_T1_2mm
(if not, use fslswapdim to make your input data of the same
orientation).
Cheers.
On 17 Dec 2008, at 18:06, Nathan Dankner wrote:
> I believe that it is a matter of incorrect registration. I am
> rather new to
> FSL, so sorry if my descriptions are inadequate. I have uploaded
> the 4D
> file, if that is of any help.
> <template_4D_GM.nii.gz>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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