Hi,

On 26 Jul 2007, at 19:42, Ryan Muetzel wrote:

> 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?

If you are just trying to compare a single subject's two timepoint FA  
images then you can just take the FA images and register them into  
their halfway point. (On the other hand, if this is to be part of a  
multi-subject longitudinal analysis in TBSS I wouldn't worry about  
this, just feed everything into TBSS as normal). However, siena_flirt  
isn't quite appropriate as it also uses the skull images as well as  
the brain images - you will need to edit this and simplify it to only  
use the FA images.

> 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.

That sounds ok, as long as you make sure in step 3 that each dataset  
is properly being aligned to the appropriate fieldmap for the unwarping.

Cheers.



>
> 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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---
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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