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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