Hi Jim
I'm not sure if there is an FSL tool. In IRTK, there is "evaluation",
which gives you mutual information and a host of other similarity
measures for a pair of images.
Hope that helps
Rolf
On Fri, Oct 02, 2009 at 04:36:55AM +0100, Jim Li wrote:
> Hi Rolf,
>
> Thanks a lot for your help. As you said, the ".mat" can catch very gross
> failures of registration. That helps.
>
> I always visually inspect the registrations, like what Mark suggested. By so
> doing I can have an opinion of which registration works better. Let's say I
> have two image volumes a and b. Using a as reference, I register b to a with
> one registration method and created a volume c; then I do the same thing
> with another registration method and created a volume d. Now I want to
> calculate the mutual information between a and c, as well as the mutual
> information between a and d. Is there a command to use in FSL to do this?
>
> I understand what Mark said that change of such numbers does not
> necessarily indicate a change in the quality of the alignment. I'm just curious
> and want to get such numbers to play with them. That's all.
>
>
> Jim
>
> On Tue, 29 Sep 2009 15:57:48 +0100, Rolf Heckemann
> <[log in to unmask]> wrote:
>
> >Hi Jim
> >
> >When you run FLIRT with default settings to register a pair of images
> >(no matter whether they are from the same subject or different ones),
> >the output represents the optimal alignment as measured by the
> >correlation ratio. You can set an option for FLIRT to use a different
> >cost function, e.g. mutual information. This then becomes the measure
> >of "goodness", and FLIRT manipulates the alignment parameters until
> >this value becomes as "good" as possible.
> >
> >Perhaps you can see now why it is difficult to answer your question.
> >
> >If you want to catch very gross failures, such as a pair of images not
> >matching at all after registration, and you want to avoid opening and
> >looking at each aligned pair, then I suggest you have a look at
> >flirt's .mat output. The numbers in there describe the
> >transformation. If you have a large number of .mat files, you may
> >recognize failed registrations as outliers in one or more of these
> >numbers.
> >
> >Hope that helps
> >
> >Rolf
> >
> >
> >On Tue, Sep 29, 2009 at 03:35:54PM +0100, Jim Li wrote:
> >> Hi Mark,
> >>
> >> Thanks a lot for the message, :)
> >>
> >> You know, I'm not doing image registration on different subjects. I have
> the
> >> same subject whose T2-weighted images and b0 images were done on the
> >> same day, and I tried two different ways to register the two image
> volumes. I
> >> just want to get some values to quantify the registration and see if there's
> a
> >> pattern. Could you suggest some ready-to-use script? Will fslmaths work?
> >>
> >> Thanks a lot,
> >>
> >> Jim
> >>
> >>
> >>
> >> On Tue, 29 Sep 2009 08:17:52 +0100, Mark Jenkinson
> >> <[log in to unmask]> wrote:
> >>
> >> >Hi,
> >> >
> >> >I'm afraid that there is no easy way to compare the quality of
> >> >registrations for different subjects. You can use mutual information
> >> >or other metrics to compare the quality of two different registrations
> >> >of the same images (this is how the registration works), but the values
> >> >are not really comparable across different registrations of different
> >> >images/subjects, and will tend to be influenced a lot by the FOV,
> >> >SNR, artefact level (e.g. amount of motion) and so on. Hence a
> >> >larger/smaller number does not necessarily indicate a change in
> >> >the quality of the alignment.
> >> >
> >> >We strongly recommend you visually inspect all your registrations.
> >> >This is definitely the best way to assess the quality of the alignment.
> >> >
> >> >All the best,
> >> > Mark
> >> >
> >> >
> >> >On 28 Sep 2009, at 14:46, Jim Li wrote:
> >> >
> >> >> Hello everybody,
> >> >>
> >> >> I have another Newbie question about registering two image volumes
> >> >> of the
> >> >> same subject using the same modality (MRI) after using FLIRT or
> >> >> other scripts.
> >> >> Can anyone give me a hint?
> >> >>
> >> >> Basicly, other than visual inspection of the two images after
> >> >> registration, are
> >> >> there ready-to-use scripts in FSL that can quantify the overall
> >> >> goodness of
> >> >> registration? I heard people use mutual information, etc. I just
> >> >> want to run a
> >> >> command to get a number (or more) to quantify the goodness of
> >> >> registration...
> >> >>
> >> >> Thanks a lot, :)
> >> >>
> >> >> Jim
> >> >>
> >
> >--
> >Rolf A Heckemann, MD PhD
> >Médecin chercheur
> >Fondation Neurodis
> >CERMEP - Imagerie du Vivant
> >Hôpital Neurologique Pierre Wertheimer
> >59 Boulevard Pinel
> >69003 Lyon
> >
> >
> >
> >1254235444
> >
> >
--
Rolf A Heckemann, MD PhD
Médecin chercheur
Fondation Neurodis
CERMEP - Imagerie du Vivant
Hôpital Neurologique Pierre Wertheimer
59 Boulevard Pinel
69003 Lyon
1254464487
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