> OR you could write a simple flirt
> transform to pre-flip the data (maybe this is best)...
Just to clarify how you do this.
For example, consider a flip in the y-direction.
You need to create a transform file that contains the following
matrix (as simple text):
1 0 0 0
0 -1 0 *FOVY*
0 0 1 0
0 0 0 1
where the *FOVY* should be replaced with the Field of View in the
y-direction, in mm. That is, if you have 128 voxels across in the
y-direction and each is 2mm long in this direction, then the matrix
you need is:
1 0 0 0
0 -1 0 256
0 0 1 0
0 0 0 1
Once you have this matrix, just apply the transform in flirt using:
flirt -in volinput -out voloutput -applyxfm -init flipmat -ref volinput
-interp nearestneighbour
where volinput and voloutput are the two avw filenames and flipmat is
the filename of the text matrix shown above.
This will flip any single volume (not a time-series though).
Cheers,
Mark
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