Hi Matt,
This helps a lot.
Thanks so much.
To improve SNR, if I get 2 acquisitions of bo and 32 directions, do I average these 2 acquisitions on the scanner or by using fslmeants or fslinterleave?
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, 3:19 PM
> The way to go about this is the
> following:
>
> Register your FA to T1 image and generate a diffusion to
> structural
> transformation matrix. Invert this transformation
> matrix with convert_xfm
> to generate a structural to diffusion transformation
> matrix. Generate your
> lesion ROIs from your structural images (I am assuming you
> have registered
> your T2 to your T1), then move that ROI to diffusion space
> using nearest
> neighbor interpolation with FLIRT and extract your
> values. It is best to
> minimize the interpolation of your data in general, and
> this method allows
> you to avoid interpolating at all.
>
> 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 2:33 PM
> To: [log in to unmask]
> Subject: Re: [FSL] DTI imaging
>
> 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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