Hi Matt,
just figured it out. Yes, I needed to brain extract my T1 before registration to FA maps, which is already brain extracted. Once I did that, then affine registration works fine.
The registered FA-to-T1 looks slightly blurred. What I am trying to do is look at MS lesions on T2 scans (vox dimensions about 1x1x3) getting ROIs and then deriving FA/MD/tract values from the FA/MD/etc maps which were originally derived from 2x2x2 images.
The question is would I lose any information on FA/MD/tract values by using interpolated registered FA-T2 maps for lesion analysis?
Grateful for all your help,
aj
--- On Fri, 3/12/10, Matt Glasser <[log in to unmask]> wrote:
> From: Matt Glasser <[log in to unmask]>
> Subject: Re: [FSL] DTI imaging
> To: [log in to unmask]
> Date: Friday, March 12, 2010, 8:04 AM
> That is very strange, it is common to
> get good registrations with even
> nonlinear registration with FA to T1. Are you brain
> extracting your images?
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> On Behalf
> Of Adil Javed
> Sent: Friday, March 12, 2010 1:25 AM
> To: [log in to unmask]
> Subject: Re: [FSL] DTI imaging
>
> Hi Matt,
> Thanks for your comments, very educational and
> helpful. When I transform FA
> to T1 or T2, the only Model/DOF that works is Translation
> (3 parameters
> model). The others, including rigid body (6 parameters) or
> more (7-9) give
> me very distorted images. Is registration by
> translation only (3
> parameters) good enough?
> many thanks,
> aj
>
> --- On Wed, 3/10/10, Matt Glasser <[log in to unmask]>
> wrote:
>
> > From: Matt Glasser <[log in to unmask]>
> > Subject: Re: [FSL] DTI imaging
> > To: [log in to unmask]
> > Date: Wednesday, March 10, 2010, 8:51 PM
> > That is not the right way to go about
> > things. You should leave the voxel
> > dimensions at 2x2x2mm and then Register the FA to the
> T1 to
> > get the desired
> > overlay. It is MUCH better to interpolate the
> > calculated data than to
> > interpolate the raw data and then calculate. This
> is
> > especially true if you
> > want to do tractography. You can easily still
> specify
> > masks in structural
> > space and then specify the structural to diffusion
> > transform.
> >
> > Peace,
> >
> > Matt.
> >
> > -----Original Message-----
> > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> > On Behalf
> > Of Adil Javed
> > Sent: Wednesday, March 10, 2010 6:20 PM
> > To: [log in to unmask]
> > Subject: [FSL] DTI imaging
> >
> > Hi,
> > for those who are experts in DTI:
> > I am acquiring DTI images on 3.0T Phillips scanner
> using 32
> > directions, FOV
> > 240, acquired matrix is 120 x 118 with acquired voxel
> > dimensions of 2x2x2.
> > In order to overlay DTI FA/MD/ or tracts on a FLAIR or
> T1
> > image, I need to
> > reconstruct the matrix to 256 with voxel RECON to 0.94
> x
> > 0.94 x 2 so they
> > align with my FLAIR or T1 images.
> >
> > Question: is this ok or do you see any problems
> with
> > this approach? By
> > reconstructing voxels down to 0.94 x 0.94 x 2 after
> they
> > are Acquired in
> > 2x2x2 size, am I losing any information?
> >
> > many thanks for your help.
> >
> > adil
> >
>
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