Hi,
I know the mask is aligned to the MNI152, but if your
reference image is not then there is no point putting
this mask in. The mask and the reference image
need to be perfectly aligned *before* the call to fnirt.
As for the "one as it shows" - I did not see any config
file in the command you sent us. You should take a
copy of the config file and remove the --ref and --refmask
lines from it before using it, as they are not appropriate
for your usage.
All the best,
Mark
On 30 Jul 2009, at 17:04, siamak wrote:
> Hi Mark,
>
> Thanks for your nice comments. The Mask is already aligned to
> MNI152. My
> images have 1mm isotropic voxel resolution the same as my reference
> MNI152
> template. The config file is a 2mm one as it shows. Is that Ok to
> use this
> config. file.
>
>
> Regards,
> Siamak
>
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