With rigid registration you are only allowing translation and rotation (6 degrees of freedom). Therefore, if you see misalignment around the ventricles you should see misalignment everywhere (if the ventricles didn't change). Is this the case? Try the registration while keeping the skulls on the images, do the skulls look aligned?
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From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Franklin, Crystal G [[log in to unmask]]
Sent: Wednesday, February 08, 2012 9:04 AM
To: [log in to unmask]
Subject: Re: [FSL] T1 to DTI Registration
I have ran rigid registration in flirt and I am still getting misalignment
around the ventricles. We would like to keep the DTI in native space.
Thank you,
Crystal
On 2/7/12 5:54 PM, "Cunningham, Dustin" <[log in to unmask]>
wrote:
>Hi Crystal,
>
>Usually you can get satisfactory registration between T1 and b0 in the
>same subject using rigid registration in flirt. May I ask why you want to
>register the T1 to DTI and not the other way around? Also, the ventricles
>should look very similar in shape in the T1 and b0 image, which is
>essentially T2 weighted.
>
>Dustin
>________________________________________
>From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of
>Franklin, Crystal G [[log in to unmask]]
>Sent: Tuesday, February 07, 2012 4:52 PM
>To: [log in to unmask]
>Subject: [FSL] T1 to DTI Registration
>
>Dear FSL,
>
>I am trying to register my subject's T1 (voxel dimensions of .8x.8x.8) to
>their DTI (voxel dimensions of 1.719x1.719x3). Unfortunately I do not
>have a T2 image or field maps. Do you suggest using the FA image or the
>b0? I have tried using both in flirt. The registration looks pretty
>good until I get around the ventricles. What is the best way to go about
>correcting this misalignment or the best procedure for registering the T1
>to DTI?
>
>Thank you,
>Crystal
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