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
>> <<a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind0910%26L%3DFSL%26E%3Dquoted-printable%26P%3D44380%26B%3D--Apple-Mail-5--864326672%26T%3Dtext%252Fplain%3B%2520charset%3DISO-8859-1%26attachment%3Dq" target="_parent" >[log in to unmask]</a>> 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
>>>> <<a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind0910%26L%3DFSL%26E%3Dquoted-printable%26P%3D44380%26B%3D--Apple-Mail-5--864326672%26T%3Dtext%252Fplain%3B%2520charset%3DISO-8859-1%26attachment%3Dq" target="_parent" >[log in to unmask]</a>> 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
>