Hi,
This is actually a fairly advanced use that we haven't really been
asked for before - it certainly isn't a standard newbie question!
Most people don't yet have reliable qforms that they want to use, but
I'm glad that you have.
So although it is not part of the standard settings, it shouldn't be too
hard to make this work. What you need to do is the following:
1 - register your t2w image to the standard and save the
transformation (say t2w2std.mat file)
2 - for each other image that you want to use the qforms to align
with the t2w image do:
flirt -in otherimage -ref t2w -applyxfm -usesqform -omat other2t2w.mat
3 - concatenate the previous transform with the one from t2w to
standard:
convert_xfm -omat other2std.mat -concat t2w2std.mat other2t2w.mat
4 - apply this concatenate transform with flirt:
flirt -in otherimage -ref standard -applyxfm -init other2t2w.mat
This should hopefully work, as the second stage saves the flirt matrix
which would align the two images based on their qforms. There could be
problems if there are conflicting sforms or missing qforms, but try it
first and let me know if you have any trouble.
All the best,
Mark
On 18 Feb 2008, at 15:17, Alessandro Daducci wrote:
> Hi everyone,
> I'm a newbie in the field of medical image analisys and I need some
> help.
> I'm trying to use FLIRT to coregister a t2w dataset to a reference
> template.
> Until now all is fine. But I can't figure out how to use the output
> affine
> matrix in order to apply the same transformation to other datasets
> of the
> same animal (I work on rats' brains). I can do all the pipeline if
> I reslice
> every dataset to the magnet isocenter and the use FLIRT to
> coregister one of
> them to the reference and then applying the .mat to all the other
> datasets.
> All theese datasets can be acquired with different orientations and
> dimension.
>
> But I'd like to do this:
> 1) export data from the scanner and save into qform field its
> transformation
> without the need to reslice at this stage;
> 2) use FLIRT to find out the affine matrix that let me to align a
> particular
> scan of the animal (t2w);
> 3) use this matrix (and the qform information from all datasets) in
> order to
> apply it to every other dataset.
>
> Is it possible?
>
> I tried both with FSL bash scripts and MATLAB, but I can't
> succesfully make
> these operation.
>
> Can someone help me please?
>
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