[MINC-users] Co-registration metric (minctracc)

[Paul GRAVEL]

Great idea!
Many thanks again!
Paul


On Fri, 29 Jan 2016, Andrew Janke wrote:

> Not as of yet. Looking at the code it would seem that the floor value
> only applies to the first input volume.
>
>   https://github.com/BIC-MNI/minc/blob/master/progs/minccmp/minccmp.c#L333
>
> It would not be a hard change to make, the code for dealing with
> ranges of input values is already in mincstats.
>
> For now I'd suggest a first pass through with minccalc setting values
> in the first to 0 if the second is below a floor value.  In the
> example below the floor values are:
>
>   input1.mnc 12.5
>   input2.mnc 23.5
>
>   minccalc -expression "(A[1] < 23.5) ? 0 : A[0]" input1.mnc
> input2.mnc input1-floor.mnc
>
>   minccmp -floor 12.5 input1-floor.mnc input2.mnc
>
>
> a
>
>
> On 29 January 2016 at 10:05, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>> Many thanks Andrew!
>>
>> I gave it a try, and it looks promising!
>> btw, is there a way to floor each volume with different values?
>>
>> Best,
>>
>> Paul
>>
>>
>>
>> On Fri, 29 Jan 2016, Andrew Janke wrote:
>>
>>> Hi Paul,
>>>
>>> Yes the output of minctracc should be able to help you. Just be aware
>>> that if you are running minctracc within something else (nlpfit,
>>> mritotal, etc) in which step sizes and other things change that the
>>> correlation will also change.
>>>
>>> You might also be interested in minccmp,  I added it some time ago for
>>> this express purpose.
>>>
>>>
>>> a
>>>
>>>
>>> On 29 January 2016 at 05:38, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>> wrote:
>>>>
>>>> Dear All,
>>>>
>>>> Hope all is well!
>>>>
>>>> Is there a metric (or metrics) to test the goodness of co-registration
>>>> with
>>>> minctracc (would that be comparing the Initial objective function val vs.
>>>> Final objective function value)?
>>>>
>>>> The reason for this question is that I am running a script that does 2
>>>> passes of a PET to PET co-registration, but sometimes the second pass
>>>> messes
>>>> things up, especially when the first pass looks good.
>>>> Thus I would like to use this metric to automatically check whether or
>>>> not
>>>> the second pass should be run at all.
>>>> Of course, I would still visually inspect the end results ;-)!
>>>>
>>>> Thanks!
>>>>
>>>> Paul
>>>>
>>>>
>>>> _______________________________________________
>>>> MINC-users at bic.mni.mcgill.ca
>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
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>>>
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