Dear Erik,
There's a tool called avwswapdim which allows you to do
all of these things and works for 4D files.
The usage is simple in that you just have to specify what the new
x,y,z axes are in terms of the old ones.
This tool is not part of the standard distrubution at the moment
but the linux binary is available at
http://www.cfn.unimelb.edu.au/nig/markj/files/avwswapdim
It does not have automatic determination of sagittal, coronal or axial
but these are easily worked out from your images.
If you are in doubt about the FSL x,y,z conventions, just do "slices"
on the image. The last 3 views will show the x-y plane (x is horizontal,
y is vertical). This should be enough to figure out the required axes.
There is also a warning printed if the left/right orientation is likely to
change (i.e. the transformation includes a reflection as well as a rotation).
If this happens but you don't want it then make sure to use the negative
version of the original L-R axis.
All the best,
Mark
P.S. Let me know if you need a non-linux version and I will compile it for you.
Erik-Jan Vlieger wrote:
> Hi,
>
> AIR5 has a tool to reorient analyze files; make them saggital, flip
> left/right, etc. I wanted to use this tool on my 4D analyze file, however, as
> AIR5 is solely 3D, it only kept the first volume of my 4D file.
>
> Does FSL include a similar tool? If not, does anyone have a suggestion on how
> to accomplish the same task?
>
> Thanks,
> Erik-Jan Vlieger
|