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FSL  July 2007

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Subject:

coregistration of FA maps

From:

Ryan Muetzel <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 26 Jul 2007 13:42:55 -0500

Content-Type:

text/plain

Parts/Attachments:

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text/plain (98 lines)

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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