Works great. Thanks for the explanation.
Gordon
On 04/23/2010 06:03 AM, Mark Jenkinson wrote:
> Hi,
>
> You just need to add the -2D option to this flirt call and it will be fine.
>
> Note that Steve's paddingsize option (setting it to more than a
> slicethickness)
> will also work, as this is what -2D internally sets. This basically
> allows the
> interpolation to treat the 2D object with some 3D thickness, which is
> necessary
> for the 3D interpolation methods to work.
>
> All the best,
> Mark
>
>
> On 23 Apr 2010, at 09:54, Junqian Gordon Xu wrote:
>
>> Mark,
>>
>> In the context of "slice by slice" registration, this will give you a
>> blank output slice (presumably because of this tiny z translation).
>>
>> flirt -in $frame$slice -ref $b0mean$slice -applyxfm -init $matAtoD
>> -out $frame"_xenc"$slice
>>
>> Regards
>> Gordon
>>
>> On 04/23/2010 03:45 AM, Mark Jenkinson wrote:
>>> Hi,
>>>
>>> Yes, there are some rounding errors in the matrix libraries that we use
>>> which generate tiny numbers like this. Given that it represents a
>>> translation
>>> of 0.61 nanometres, I normally find that this doesn't make any
>>> difference to
>>> anything - even when concatenated with other transformations with
>>> similar
>>> rounding errors. Do you have an example of where this is actually
>>> important?
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>> On 23 Apr 2010, at 08:38, Junqian Gordon Xu wrote:
>>>
>>>> flirt -in $frame$slice -ref $frame"1"$slice -out $frame"_xenc"$slice
>>>> -omat $tempmat -2D
>>>>
>>>> $tempmat:
>>>>
>>>> 0.989301 -0.145891 0 3.07181
>>>> 0.145891 0.9893 0 -5.26495
>>>> 0 0 1 6.10647e-07
>>>> 0 0 0 1
>>>>
>>>> When running a slice by slice flirt -2D registration, the output mat
>>>> sometimes (seems randomly) contains a small z translation (e.g.
>>>> 6.10647e-07, see above). The output $frame"_xenc"$slice is fine though.
>>>>
>>>> This z translation causes trouble when one tries to concatenate
>>>> transformations later on. I currently use the following line to reset
>>>> the z-trans value back to 0.
>>>>
>>>> awk 'NR==3 {$4=0}1' $tempmat > $mat
>>>>
>>>> I don't think it's of a high priority to be investigated or fixed, but
>>>> thought it's good to point it out for people going down the same route.
>>>>
>>>> Regards
>>>> Gordon
>>>>
>>>
>>
>
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