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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