Dear Steve,
yes, that works!
Thanks a lot,
Oliver
Steve Smith schrieb:
> 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
> ---------------------------------------------------------------------------
>
>
--
Dr. med. Oliver C. Singer
Klinik für Neurologie
Zentrum der Neurologie und Neurochirurgie
Johann Wolfgang Goethe-Universität
Schleusenweg 2-16
60528 Frankfurt am Main
Tel: (+49) (0)69-6301-6895
Fax: (+49) (0)69-6301-6842
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