Hello,
This is a question similar to post# 010866, from April 2007 (text pasted
below).
We have collected cross-sectional and longitudinal DTI data and would like
to coregister the data.
In the post below, from what I can tell, it was recommended that the half
xfm's be used with flirt. In the siena_flirt src code, it seems things are
done slightly different than that(average the full xfm's first, then take
the halfway's). Would you recommend one way over the other for DTI data
(substituting flirt for the pairreg steps in siena_flirt, I'm guessing)?
Do you recommend starting with raw data (say the b=0, and apply the xfm's
to the 4D data), or starting with FA maps?
I have been working on coregistering two DTI scans, collected at the same
time-point. These scans have slightly different echo spacings and thus
slightly different susceptibility artifact. The differences in
susceptibility artifact seem to be causing misalignments between two data
sets. I get a similar registration whether or not I unwarp the data with a
fieldmap. I am able to get considerably better registration if I:
1) apply the half xfm to the 4D data based on the b=0 images.
2) choose 1 b=0 image and apply eddy_correct to both 4D data sets based on
that single b=0
3) run fugue/dtifit/bedpost from here.
Are there any major flaws to this method? The two DTI scans are identical
other than the echo spacing and number of directions.
Any help/suggestions is much appreciated!!
-Ryan
Date: Wed, 4 Apr 2007 12:22:21 +0200
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Sender: FSL - FMRIB's Software Library <[log in to unmask]>
From: Oliver Singer <[log in to unmask]>
Subject: Re: Coregistration of FA-maps
In-Reply-To: <[log in to unmask]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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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