Hi - the halfway transforms are probably correct - all you need to do
is to select the SAME image (presumably the higher resolution /
larger one) as the "reference" when you apply the halfway transforms
- then the two output images should be in the same space and have the
same dimensions.
Cheers.
On 9 May 2007, at 12:56, Oliver Singer wrote:
> Dear FSL-folks,
>
> I have (again) a question concerning the realignment of two FA-
> maps. My first approach using FLIRT for rigid body (6 param)
> realignment went well, I used the transformation matrix and ran
> FLIRT again for both FA maps with the forward half transform and
> with the backward half transform data. The reason for this second
> step (realigning both maps to "halfways") was that there is an
> inherent step of smoothing when using FLIRT and it seems plausible
> to smooth both FA maps in a similar way to prevent bias.
>
> The actual problem is as follows: I have two FA-maps with different
> scalings (the slice thickness is different) and I want to
> coregister both FA-maps which works quite fine using the 12 param
> affine model of FLIRT. Again, I want to do the halfway transform
> step using the command (flirt -in in.img.nii.gz -ref ref.nii.gz -
> out out.nii.gz -applyxfm -init halfway_forward.mat) but I have the
> impression that the information concerning the scaling is lost,
> since FSL view prohibits the overlaying of the new created halfway-
> image on the reference image. I guess that I have to consider the
> scaling factors, but I do not know how. Following I copied the
> rotation and translation matrix. Up to now, I only used the forward
> (backward) half transform data.
> Thanks in advance for your help!
> Yours, Oliver Singer
>
> $ avscale --allparams dti_FA_zwei_affine12.nii.mat
> Rotation & Translation Matrix:
> 0.987698 0.105347 -0.115563 -19.034700
> -0.124221 0.977473 -0.170632 23.948400
> 0.094985 0.182889 0.978534 -37.706000
> 0.000000 0.000000 0.000000 1.000000
>
> Rotation Angles (x,y,z) [rads] = -0.172640 0.115822 0.106258
>
> Translations (x,y,z) [mm] = -19.034700 23.948400 -37.706000
>
> Scales (x,y,z) = 1.001994 1.022542 1.025332
>
> Skews (xy,xz,yz) = 0.013557 0.009088 0.030568
>
> Average scaling = 1.01662
>
> Determinant = 1.05054
> Left-Right orientation: preserved
>
> Forward half transform =
> 0.997907 0.062887 -0.050848 -10.348140
> -0.060228 1.005081 -0.073460 10.938658
> 0.050480 0.091907 1.008767 -18.999305
> 0.000000 0.000000 0.000000 1.000000
>
> Backward half transform =
> 0.995672 -0.066540 0.044557 11.877758
> 0.055957 0.986308 0.075207 -8.780949
> -0.054172 -0.086402 0.980708 19.017314
> 0.000000 0.000000 0.000000 1.000000
>
>
>
>
>
> Christian Beckmann schrieb:
>> Hi
>>
>> you just run flirt with the -applyxfm -init options:
>>
>> flirt -in in.img.nii.gz -ref ref.nii.gz -out out.nii.gz -applyxfm -
>> init halfway_forward.mat
>>
>> That should do the trick
>> cheers
>> christian
>>
>> On 4 Apr 2007, at 11:22, Oliver Singer wrote:
>>
>>> 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
>>>>>>
>>>>> ------------------------------------------------------------------
>>>>> ------
>>>>>
------------------------------------------------------------------------
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
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