Hello Mark
> Have you tried it with brain extraction run on both images?
> We generally recommend that. I suspect that this will fix it.
>
> Also, for within-subject registration you should use 6 dof, not 12.
>
> If this still doesn't fix it, and if you have good information from
> your DICOM conversion, then try -usesqform as that can sometimes
> be a good option to try.
Yes it is a within-subject registration and I agree with you that I should have
been using 6. The reason I use 12 is because the two images were acquired
on different field strengths, so distortions are different and I reasoned that
12 is more suitable than 6. Would you agree with this?
About the usesqform switch. Do you mean to imply that without the switch
the image orientation informaiton is ignored (to allow backward
compatibility with
Analyze)? With the switch, the orientation is taken into account?
Could you ellaborate on
what the switch does.
And finally, yes, combining bet with flirt -usesqform helped.
Thank you very much for your help
Lazar
>
> All the best,
> Mark
>
>
> On 14 Mar 2011, at 18:53, Lazar Fleysher wrote:
>
>> Hello everybody,
>>
>> I am sure, this question have been answered somewhere, but for some
>> reason I cannot find a similar topic in the forum archive.
>>
>> Basically, I have a high resolution T1-weighted image (MPRAGE) and
>> would like to coregister a low resolution T2-weighted image to T1.
>> This is a standard problem.
>> I use flirt to do it and the result I get is T2 image rotated by 90
>> degrees around LR axis.
>> (see the attached image) Grayscale is T1 and color is T2.
>>
>>
>> The command which was used to attempt the coregistration is this
>>
>> flirt -in t2image.nii.gz -ref t1image.nii.gz -out coregimg2 -omat
>> transformation2.mat -bins 256 -cost mutualinfo -searchrx -18 18
>> -searchry -18 18 -searchrz -18 18 -dof 12 -interp trilinear
>> -searchcost mutualinfo
>>
>> Because the images intially a almost "coregistered" I have restricted
>> the angular search to speed up the calculation.
>>
>> Could some one suggest what I did wrong or maybe some options which I
>> should use to attempt to resolve
>> the problem?
>>
>> Thank you very much for your help
>>
>> Lazar
>> <Screenshot-5.jpg>
>
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