Hi,
Currently fnirt is not optimised for doing registrations between two
high-resolution images, but it can be made to work.
You should be using a config file with fnirt when doing any registration
with it. If your images are both T1 images then take the
T1_2_MNI152_2mm.cnf
config file from $FSLDIR/etc/flirtsch and remove the line specifying the
reference image (--ref) and reference mask (--refmask) as these are
not relevant for your case. You can then specify your own reference
image
on the command line (in addition to the config file) and a reference
mask
if you wish. However, the reference mask *must* be pre-aligned with the
reference image, so if you are using image2 as your reference then you
cannot use a reference mask in MNI152 space unless image2 is already
aligned to that space.
Also, you do not need to specify the subsampling scheme explicitly, as
that is in the config file.
Hope this helps.
All the best,
Mark
On 28 Jul 2009, at 20:49, siamak wrote:
> Hi,
>
> I am using fnirt command to register to T1 IBSR images in a masked
> region. I
> am using a command as follows:
>
> flirt -in image1_brain.nii -ref image2_brain.nii -omat affine1.mat -
> out
> image1_flirted.nii
> fnirt --in=image1.nii --ref=image2.nii --iout=image1_fnirted.nii --
> cout=warp --
> refmask=MNI152lin_T1_1mm_subbr_mask.nii --aff= affine1.mat --
> sumsample=
> 8,4,2,2
>
> I expect that image1_fnirted.nii has better alignment specially in
> subcortical
> region (as applying refmask) than image1_flirted.nii. But, the
> results do not
> support this. After applying some processing to evaluate the accuracy,
> image1_fnirted.nii has a volume around 25% more than
> image1_flirted.nii in
> subcortical region and has not a good match to the reference image.
> I mean,
> fnirt expands the volume and does not result in a good alignment in
> that area.
> I checked it several time using IBSR datasets that I have the
> segmented
> image as gold standard.
> Is there any other settings in fnirt command that result in a robust
> dependable
> results?
>
> Siamak Yousefi
>
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