Thanks Matt,
you're the best!
aj
--- On Sat, 3/13/10, 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: Saturday, March 13, 2010, 10:22 AM
> You would absolutely not average them
> on the scanner because you cannot
> correct for subject motion between the averages. You
> would first merge them
> in the time dimension with fslmerge, run eddy_correct on
> the merged file,
> split them back out with fslroi, and average them with
> fslmaths (add them
> and divide by 2). There are example scripts posted on
> this list that
> describe this process in detail.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> On Behalf
> Of Adil Javed
> Sent: Saturday, March 13, 2010 1:28 AM
> To: [log in to unmask]
> Subject: Re: [FSL] DTI imaging
>
> 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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