Dear Leo,
Yes, the first number is the cost value.
You can suppress the printing of the matrix by using the -omat
option with a dummy name.
All the best,
Mark
On 2 May 2011, at 20:16, Yiou Li wrote:
> Dear Mark,
>
> Thanks very much for the detailed comments!
>
> Here is what I got by running flirt with the schedule file:
>
>>> flirt -in inputfile -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz -init xmat_T1_to_MNI152_2mm -out test1 -schedule $FSLDIR/etc/flirtsch/measurecost1.sch
>
> 0.0669054 0.000000 -0.000000 0.000000 0.000000 0.000000 0.000000
> 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000
>
>
> Final result:
> 0.971940 -0.035396 0.008270 -1.957650
> 0.033794 0.891260 0.081227 -0.548800
> -0.004905 -0.131739 0.998848 5.771490
> 0.000000 0.000000 0.000000 1.000000
>
> I guess the first number in the first output row is the cost value,
> please kindly confirm.
>
> Best,
> Leo
>
>
> On Sat, Apr 30, 2011 at 1:06 AM, Mark Jenkinson <[log in to unmask]> wrote:
>> Dear Leo,
>>
>> This is a fairly standard question and the answer is that
>> there is no good answer! The metrics you suggest in 1
>> and 2 are flawed, as you pointed out. Using the same
>> metric that the registration uses won't tell you much, as
>> it is explicitly optimised by the registration method.
>> However, you can get cost function values from FLIRT
>> by using the schedule file: $FSLDIR/etc/flirtsch/measurecost1.sch
>>
>> This returns the cost for the given -init matrix (this matrix
>> should be the output of the registration step you've run
>> previously). It is difficult to interpret the cost function values
>> when comparing different images, as there may be differences
>> in the image intensities that modify the overall cost without
>> necessarily affecting the accuracy of the registration.
>>
>> The best solution to assess the quality of the registration is
>> to inspect the results by eye, or use manually placed landmarks
>> and quantify the displacement errors of the landmarks after
>> registration. There are quite a few papers dealing with the
>> assessment of registration quality (often for comparing methods)
>> which you can read more about if you are interested.
>>
>> All the best,
>> Mark
>>
>>
>> On 30 Apr 2011, at 00:24, Yiou Li wrote:
>>
>>> Dear FSLers,
>>>
>>> I want to assess the quality of the FLIRT registration of different T1
>>> images to MNI152_T1 template. Could you please advise what is a good
>>> numeric metric for the assessment?
>>>
>>> I am thinking of the following ones:
>>>
>>> 1. Sum of mean square error between the registered and the reference
>>> image (this might not be a good one because I found the intensity
>>> scales of the two images are quite different).
>>>
>>> 2. Determinant of the transformation matrix (I know this has been used
>>> to evaluate local deformations, but large deformation could result in
>>> good registration quality, so this metric is not relevant?)
>>>
>>> 3. The final cost function value obtained by FLIRT (corrate, mutual
>>> information, etc.) However, flirt doesn't output this information, is
>>> there easy way to get this value?
>>>
>>> Any comment on this will be appreciated.
>>>
>>> Leo
>>>
>>> PS. Congrats to new royal couple ^_^
>>>
>>
>
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