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FSL  October 2009

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Subject:

Re: quantify registration evaluation

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 2 Oct 2009 08:24:23 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (23 lines) , measurecost1.sch (23 lines) , Unknown Name (187 lines)

Hi,

Yes, you can get this information from FLIRT.
Just do:
   flirt -in resampled_image -ref refimage -schedule measurecost1.sch
You can also select the similarity metric you want with -cost ...

The measurecost1.sch file has been posted on the list before, but
I'm attaching another copy here.  Just save it (as plain text)
somewhere and give the full path in the command above.

The cost value is the first number printed.  If you want to  
automatically
select only this then you can do:
    flirt .... | head -1 | cut -f1 -d' '
with the above flirt command.

All the best,
	Mark





On 2 Oct 2009, at 07:26, Rolf Heckemann wrote: > 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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