Hi,
I think the registration from FLAIR image into MNI space can be
carried out in a hierarchical way
in FSL:
1. FLAIR to MPRAGE, use rigid or affine registration , and produce
affined-transformed flair
2. MPRAGE to MNI use nonlinear registration
3. displacement field from step 2 can used to further transform
affined transformed flair into
MNI.
Also there is a method for automated WMH segmentation and localization.
" A fully automated method for quantifying and localizing white matter
hyperintensities on MR images."
Psychiatry Research: Neuroimaging, Volume 148, Issue 2-3, Pages 133-142
Good luck,
Minjie Wu
On Tue, Mar 18, 2008 at 11:45 AM, Peter Kochunov <[log in to unmask]> wrote:
> I think you should have little troubles registering two datasets. One step
> you can do to insure stability is reslicing the FLAIR data into 1x1x1
> resolution before regestering it to T1w. Also you might want to play with
> the cost function in flirt. The normalized correlation don't seem to work as
> well as say mutual info.
>
> pk
> ----- Original Message -----
> From: "Agnieszka Burzynska" <[log in to unmask]>
> To: <[log in to unmask]>
>
>
> Sent: Tuesday, March 18, 2008 10:39 AM
> Subject: Re: [FSL] White matter hyperintensity and FLAIR processing
>
>
> > Dear Peter,
> > Thank you a lot for your email.
> > I can do without the automation (will do manual identification of affected
> > tissue), but I would like to have my FLAIR images in the MNI space. Do you
> > know if anyone does such registration with 5mm slice thickness? I know you
> > had 1mm isovoxel in your recent study and others with my parameters just
> > do
> > manual tracing on FLAIR image + multiply by slice gap to get the WMH
> > volume.
> >
> > Do you know if I will get this registration well in FLIRT and my MPRAGE or
> > shall I use a 1x1x1 T1-WI of these subjects (I may get them, but acquired
> > in
> > different MRI session- or will it cause even more problems with my FLAIR
> > quality?). I am not too familiar with FLIRT yet.
> >
> > Thanks a lot,
> > Aga
> >
> >
> > On 18.03.2008 14:33 Uhr, "Peter Kochunov" <[log in to unmask]> wrote:
> >
> >> Aga,
> >>
> >> Unfortunatly, I don't think automated processing will be possible with
> >> this
> >> dataset. The only workable approach to do automated HWM lesion
> >> segmentation
> >> is by the use of T2-maps produced by the multi-echo sequences.
> >> pk
> >> ----- Original Message -----
> >> From: "Agnieszka Burzynska" <[log in to unmask]>
> >> To: <[log in to unmask]>
> >> Sent: Tuesday, March 18, 2008 7:09 AM
> >> Subject: [FSL] White matter hyperintensity and FLAIR processing
> >>
> >>
> >>> Dear all,
> >>> I am searching for the most straightforward way to estimate the WMH load
> >>> in
> >>> my subjects.
> >>> 1) Was there any follow-up on the message from 2002? (see below)
> >>> 2) My FLAIR images have resolution 1.3x0.9x5mm and my MPRAGE 2x2x1mm.
> >>> Does
> >>> it mean I will have hard time in registering them to MNI?
> >>>
> >>> Thank you!
> >>>
> >>> Aga
> >>>
> >>>
> >>> On Mon, 22 Jul 2002, Wei Wen wrote:
> >>>
> >>>> Dear Steve,
> >>>>
> >>>> It may be possible to extract (segment) white matter hyperintensity
> >>>> (FLAIR
> >>>> sequence) using a combination of bet, fast etc. as discussed at FSL
> >>>> course
> >>>> in Melbourne. Could I send you a couple of such images and see if you
> >>>> could
> >>>> tweak the programs (or come up with some suggestions) for this purpose?
> >>>>
> >>>> Many thanks,
> >>>>
> >>>> Wei Wen
> >>>> NPI, Prince of Wales Hospital/UNSW
> >>>> Australia
> >>>>
> >>>>
> >>>
> >
>
--
-Minjie
|