Hi,
This looks all correct to me.
Can you run both:
fslhd t1_brain
and
fslstats t1_brain -w
and send us the output.
It is possible that you are just over the
automatic checking threshold and that it
isn't serious, in which case the --force
flag with invwarp would solve the problem.
However, it is worth checking the above
output first.
All the best,
Mark
On 18 Jun 2010, at 18:37, Rajagopalan, Venkateswaran wrote:
>
> Hi All,
>
> I used the following to commands to do non-linreg between my T1 and
> MNI space and i would like to now bring MNI to my t1 space where i
> encountered the problem with invwarp (i saw archives about this but
> my case is different from the one in the archive)
>
> flirt -ref MNI152_T1_2mm_brain.nii.gz -in t1_brain.nii.gz -out
> T1_in_MNI_space_linreg -omat T1_2_MNI_linreg.mat
>
> fnirt --ref=MNI152_T1_2mm --in=t1.nii --aff=T1_2_MNI_linreg.mat --
> iout=T1_in_MNI_space_nonlinreg --cout=T1_2_MNI_nonlin --
> config=T1_2_MNI152_2mm.cnf
>
> invwarp -w T1_2_MNI_nonlin.nii.gz -o MNI_2_T1_space_inversewarp -r
> t1_brain.nii.gz
>
> WARNING!! Reference image has large non-zero ROI. Check that BET has
> run successfully on this
>
> i have used the same t1_brain in both the cases after BET (and some
> manual edits to the brain to remove left over non-brain regions).
> The same commands (invwarp too) ran without any problem in another
> subject which is processed identically like the one above
>
> What am i doing wrong here.
>
> Thanks
>
> venkat
>
>
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