Dear Mark,
thanks for your help concerning the realignment of the FA-maps using the
half-transformation matrices. Seems the best option to me.
However, I have some "technical" questions concerning the way to do this:
I ran FLIRT on the two FA-images. Using avscale I get the matrices for
forward and backward half transform as follows:
Forward half transform =
0.999691 -0.024777 -0.002129 4.972743
0.024866 0.997103 0.071886 0.730804
0.000342 -0.071916 0.997410 3.274879
0.000000 0.000000 0.000000 1.000000
Backward half transform =
0.999691 0.024866 0.000342 -4.990497
-0.024777 0.997103 -0.071916 -0.369960
-0.002129 0.071885 0.997411 -3.308346
0.000000 0.000000 0.000000 1.000000
My question now is how to apply these matrices to receive the
halfway-FA-images? Is it using the convert_xfm option or the
img2imgcoord option?
Sorry for this probably basic question.....
Yours Oliver
Mark Jenkinson schrieb:
> Hi,
>
> There are other interpolation schemes such as nearest neighbour
> or sinc, but they each have some disadvantages too, and will
> make one image qualitatively different from the other. The
> smoothing is inherent in trilinear interpolation, some rather
> ugly discontinuities occur with nearest neighbour and some
> ringing and/or variable smoothing can occur with sinc.
>
> An alternative is to transform both images to a half-way
> point, this equalising the interpolation effects. This is
> what is done in SIENA, and you can do the same by extracting
> the forward and backward half-transformation matrices from
> the output of "avscale" as run on your original transformation
> matrices.
>
> That's what I would recommend.
>
> All the best,
> Mark
>
>
>
>> Hi,
>> You can change the interpolation scheme to nearest neighbour.
>> (Advanced options in the gui)
>>
>> Saad.
>>
>>
>> On 2 Apr 2007, at 14:28, Oliver Singer wrote:
>>
>>
>>> Hi,
>>>
>>> I am trying to realign FA-maps of one subject, who was scanned at
>>> two different time points. After running BET I am using FLIRT for
>>> realigning (rigid body transform, 6D OF) the B0 images (extracted
>>> from the DTI data set) of the second measurement to the B0 images of
>>> the first measurement and as secondary images to apply the
>>> transform to I take the FA maps of the second measurement.
>>> The realignment works fine, but the FA-map of the second
>>> measuresment (the realigned one) was "smoothed" during the process.
>>> Since the first FA-map was not processed, the two maps differ in
>>> terms of their "resolution / smootheness".
>>> Is there a way either to turn off the "smoothing" during the
>>> realignment or to smoothe the first FA-map (which was not
>>> transformed) in a similar way? (I do not want to realign all images
>>> to a "standard brain" due to gross pathology)
>>> Any help is appreciated,
>>>
>>> Yours , Oliver
>>>
>> ------------------------------------------------------------------------
>> ---
>> Saad Jbabdi,
>> Postdoctoral Research Assistant,
>> Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222545 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~saad
>> ------------------------------------------------------------------------
>>
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