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
>>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>>
|