As MJ said, this is a cost function that helps for registration across different modalities... You can set this in the flirt advanced options.
Cheers,
Gwenaelle
> De: Sven Haller <[log in to unmask]>
> Objet: Re: [FSL] Normalize DATSCAN to MNI (ideally non-linear)
> Ą: [log in to unmask]
> Date: Mercredi 16 mars 2011, 19h56
> PS
> What is mutual information?
>
> On 16.03.2011, at 12:54, Gwenaėlle DOUAUD wrote:
>
> >
> >
> > Hi Svan,
> >
> > my 2p on this...
> >
> > When I had to deal with F-Dopa in controls and
> patients, I found that a linear registration with mutual
> information to the T1w, followed by the application of the
> warp derived from the optimised VBM was working very well...
> The other advantage is that you will also place DAT and VBM
> in the same space, so that if you want to regress out
> voxel-wise the VBM "confound", you'd be able to do so.
> >
> > Cheers,
> > Gwenaelle
> >
> >
> >
> >> De: Sven Haller <[log in to unmask]>
> >> Objet: Re: [FSL] Normalize DATSCAN to MNI (ideally
> non-linear)
> >> Ą: [log in to unmask]
> >> Date: Mercredi 16 mars 2011, 10h55
> >> Dear Mark, Cornelius and Andreas
> >>
> >> Thanks a lot for you input!
> >>
> >> So far I have no experience with DatScans, and I
> highly
> >> appreciate your comments!
> >>
> >> My idea is to do a multi-modal analysis of GM
> (VBM), WM
> >> (TBSS), and DatScan
> >>
> >> Concerning DatScan, I fully agree with the
> concerns of
> >> Cornelius. The pattern is quite different from
> the
> >> anatomical boundaries of the basal ganglia, in
> particular in
> >> patients.
> >> In a previous study, we (together with Andreas)
> used TBSS
> >> preprocessing of DTI to derive a non-linear
> transformation
> >> matrix dominantly driven by the deep white matter
> >> structures. We then applied this matrix to SWI
> images
> >> (linear SWI to DTI, non linear to MNI using the
> TBSS
> >> transformation matrix). The results looked quite
> nice. So I
> >> was hoping to do the same thing i.e. linear
> DatScan to FA.
> >> The problem here in my view is the very peculiar
> image
> >> contrast of the DatScan images. My hope is that by
> this
> >> approach I could avoid some problems of
> normalization
> >> related to the decreased uptake predominantly in
> the
> >> posterior parts in patients.
> >>
> >> Concerning the other question by Cornelius, I want
> to use a
> >> control ROI in occipital area (after spatial
> registration)
> >> and calculate a ratio for each voxel.
> >>
> >> In the literature, I now found this link
> >> http://jnm.snmjournals.org/cgi/reprint/48/9/1459.pdf
> >>
> >> The authors however use essential tremor (ET)
> patients. In
> >> my limited experience of DatScans, I understand
> that the
> >> variability of uptake in this pathology is
> considerably less
> >> pronounced as compared to Parkinson patients -
> hence less
> >> problems for the spatial registration. I am thus
> not sure
> >> whether this approach can be applied to my dataset
> ( also it
> >> was done in SPM2 :-( )
> >>
> >> I would like to do randomize analyses of GM (VBM),
> WM
> >> (TBSS) and DatScan in the same subjects, therefore
> I would
> >> like to pre-process all data in FSL and
> co-register into MNI
> >> space
> >>
> >> Thanks a lot for your help
> >>
> >> Sven
> >>
> >>
> >> On 16 mars 2011, at 11:18, Mark Jenkinson wrote:
> >>
> >>> Dear Cornelius and Sven,
> >>>
> >>> OK, I've seen Sven's images now and have a
> much better
> >> feel for it.
> >>> The segmentation approach for an individual
> structural
> >> sounds flawed
> >>> based on Cornelius's observation that the
> DaTScan does
> >> not show
> >>> all the structure borders clearly.
> However, the
> >> good news is that from
> >>> the images it is clear that you can find the
> whole
> >> brain in the scan
> >>> and there main boundaries (at least
> brain/non-brain)
> >> are shown OK.
> >>> There is clearly a hot-spot in the middle of
> the scan,
> >> but that can be
> >>> dealt with by (a) hoping that the multi-modal
> cost
> >> functions (mutual
> >>> information, etc.) will just be OK with this,
> (b)
> >> "inverse" thresholding
> >>> the image so that intensities over a certain
> threshold
> >> are capped at
> >>> that value (thus eliminating the bright
> spots), or (c)
> >> using a basal
> >>> ganglia drived mask (from an individual
> segmentation
> >> or a standard
> >>> space) to do cost-function weighting and set
> these
> >> areas to zero
> >>> in the weight (thus ignoring their
> contribution to the
> >> overall alignment).
> >>>
> >>> I think that there is a good chance that one
> of these
> >> options would work.
> >>>
> >>> All the best,
> >>> Mark
> >>>
> >>> P.S. I wrote this before seeing Cornelius's
> linked
> >> images, which are
> >>> worse than the one Sven sent wrt brain
> >> boundaries. Hopefully
> >>> most data looks like Sven's images, although
> it still
> >> might be possible
> >>> to register the images that Cornelius
> sent. The
> >> outer border of the
> >>> brain is a very good boundary for
> registration
> >> within-subject.
> >>>
> >>>
> >>> On 16 Mar 2011, at 10:10, Cornelius Werner
> wrote:
> >>>
> >>>> Dear Mark,
> >>>>
> >>>> that's precisely why I think this will not
> work -
> >> the boundaries are
> >>>> NOT equal. In pathological DatScans the
> volume
> >> typically gets smaller
> >>>> (particularly the "tail" towards the
> occiput),
> >> while the anatomical
> >>>> structure stays the same. See this link
> for an
> >> example:
> >>>>
> >>>> http://www.medscape.com/viewarticle/735875
> >>>>
> >>>> or simply google DaTScan in an image
> search. While
> >> I am certainly not
> >>>> an PET expert, I seem to remember that
> DaTScans
> >> are somewhat difficult
> >>>> to analyze automatically. In our routine,
> we get
> >> semiquantitative
> >>>> results by our nuclear medicine staff at
> best.
> >>>>
> >>>> Cheers,
> >>>> Cornelius
> >>>>
> >>>> On Wed, Mar 16, 2011 at 10:50 AM, Sven
> Haller
> >> <[log in to unmask]>
> >> wrote:
> >>>>> Dear Mark
> >>>>>
> >>>>> Thanks a lot
> >>>>> Try this link. I hope that it works
> >>>>> http://gallery.me.com/sven.haller/100063
> >>>>>
> >>>>> Sven
> >>>>>
> >>>>> On 16 mars 2011, at 10:20, Mark
> Jenkinson
> >> wrote:
> >>>>>
> >>>>>> Dear Sven,
> >>>>>>
> >>>>>> It will all be about whether you
> can see
> >> details in the images of
> >>>>>> anatomical boundaries like in the
> MRI or
> >> not. Certainly the more
> >>>>>> "different" the images are and the
> less
> >> details you have in them
> >>>>>> the more it will be absolutely
> essential
> >> to register them to another
> >>>>>> within-subject image (using 6 dof
> or
> >> similar) as non-linear registration
> >>>>>> requires highly detailed images
> that show
> >> the same structures in
> >>>>>> each.
> >>>>>>
> >>>>>> One approach might be (but I can't
> say for
> >> sure without seeing the
> >>>>>> images) to segment the basal
> ganglia in
> >> the T1-weighted image and
> >>>>>> use this as a registration target.
>
> >> However, this would only be appropriate
> >>>>>> if the DATSCAN clearly showed only
> these
> >> boundaries and had them
> >>>>>> close to the anatomical
> boundaries.
> >>>>>>
> >>>>>> As for showing an image - can you
> post it
> >> somewhere on the web and
> >>>>>> put the link to it in the
> email. It
> >> is not possible to attach anything but the
> >>>>>> smallest attachments to the list
> (to avoid
> >> everyone's inbox getting swamped).
> >>>>>>
> >>>>>> All the best,
> >>>>>>
> Mark
> >>>>>>
> >>>>>>
> >>>>>> On 16 Mar 2011, at 09:10, Sven
> Haller
> >> wrote:
> >>>>>>
> >>>>>>> Dear Mark
> >>>>>>>
> >>>>>>> Thank you very much for your
> e-mail
> >>>>>>>
> >>>>>>> In fact the DaTScans are very
> >> different to "normal" SPECT or PET, e.g. FDG PET.
> In the
> >> latter you have activity in the entire brain, so I
> think
> >> that normalization to a T1 (maybe after BET)
> should be
> >> possible (although I have no personal experience
> here).
> >>>>>>>
> >>>>>>> The image of a DaTScan is
> >> fundamentally different (see attachment). In fact
> activity
> >> is present only in the basal ganglia. I think that
> therefore
> >> the procedure to normalize the scans should be
> very
> >> different.
> >>>>>>>
> >>>>>>> I like FSL, and I would like
> to
> >> analyze VBM and TBSS. Therefore it would be best
> to analyze
> >> the DaTScan also in FSL, followed by a RANDOMISE
> analysis
> >>>>>>>
> >>>>>>> Any help is highly
> appreciated
> >>>>>>>
> >>>>>>> Sven
> >>>>>>>
> >>>>>>> PS: The image was refused (too
> large).
> >> Maybe I can send it to you in another way??
> >>>>>>>
> >>>>>>>
> >>>>>>> On 16 mars 2011, at 09:29,
> Mark
> >> Jenkinson wrote:
> >>>>>>>
> >>>>>>>> Dear Sven,
> >>>>>>>>
> >>>>>>>> I have no direct
> experience of
> >> DATSCANs but I assume they are similar
> >>>>>>>> to general SPECT or PET
> >> scans. We have had success registering
> >>>>>>>> SPECT/PET to MRI
> before. It
> >> is always better to register the SPECT/PET
> >>>>>>>> to that subject's MRI
> using 6 DOF
> >> with FLIRT and a cost function like
> >>>>>>>> mutualinfo or
> normmi. I
> >> would normally choose the best T1-weighted
> >>>>>>>> scan as the reference, but
> it may
> >> depend on what features are most
> >>>>>>>> clearly seen in your
> DATSCAN.
> >>>>>>>>
> >>>>>>>> Once you've got a good
> >> registration of your DATSCAN to your MRI,
> >>>>>>>> then you can register the
> MRI to
> >> the MNI standard space image.
> >>>>>>>> This registration can be
> done with
> >> non-linear (FLIRT then FNIRT)
> >>>>>>>> whereas it is usually
> very, very
> >> bad to try and register the SPECT/PET
> >>>>>>>> with non-linear directly
> as there
> >> are very few features there to drive
> >>>>>>>> that registration.
> >>>>>>>>
> >>>>>>>> When you have the two
> >> registrations then you can combine them with
> >>>>>>>> convertwarp to get a
> non-linear
> >> registration from the DATSCAN to
> >>>>>>>> the MNI standard space.
> >>>>>>>>
> >>>>>>>> I do not know what you
> want in
> >> terms of a "specific template of the
> >>>>>>>> basal ganglia" but we have
> several
> >> atlases in FSL, and they include
> >>>>>>>> basal ganglia
> parcellations.
> >>>>>>>>
> >>>>>>>> All the best,
> >>>>>>>>
> Mark
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On 16 Mar 2011, at 07:37,
> Sven
> >> Haller wrote:
> >>>>>>>>
> >>>>>>>>> Dear all
> >>>>>>>>>
> >>>>>>>>> I would like to
> normalize
> >> DATSCANs to MNI standard space
> >>>>>>>>> I also have 3DT1 (easy
> using
> >> FSLVBM) and DTI (easy using TBSS).
> >>>>>>>>>
> >>>>>>>>> Are there any existing
> tools
> >> for FSL for DATSCANs?
> >>>>>>>>> Is there a specific
> template
> >> of the basal ganglia?
> >>>>>>>>> Any experience whether
> it is
> >> better to perform a linear registration DATSCAN to
> DTI, and
> >> then use the non-linear registration of TBSS, or
> better
> >> directly register DATSCAN to NMI? In that case,
> how? Linear
> >> or non-linear?
> >>>>>>>>>
> >>>>>>>>> Any help is highly
> >> appreciated
> >>>>>>>>>
> >>>>>>>>> Sven
> >>>>>>>>>
> >>>>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Dr. med. Cornelius J. Werner
> >>>> Department of Neurology
> >>>> RWTH Aachen University
> >>>> Pauwelsstr. 30
> >>>> 52074 Aachen
> >>>> Germany
> >>>>
> >>
> >
> >
> >
>
|