Hi,
Flirt, bet and some other programs don't work well with
animal images I'm afraid. For flirt the reason is that
the dimensions are too small for the default scalings of
8mm,4mm,2mm,1mm in the multi-resolution stages. There is
a simple work-around for this which is to artificially
increase your voxel size to make the brain "human-sized".
This is described briefly on the FAQ:
http://www.fmrib.ox.ac.uk/fslfaq/#feat_animal
We should be releasing a new version of flirt soon that
will hopefully work automatically with animal images, but
for the moment this is the best solution.
All the best,
Mark
On 15 Oct 2004, at 20:09, Thomas L. Arnow wrote:
> Hello,
> I am a new fsl user trying to align rat images with FLRIT and get
> the
> warning message shown below, and no output is produced. I belive I am
> using
> the system correctly because I successfully aligned two human PET
> images in
> a similar manner. I viewed the images and they look correct. Several
> slices
> may be zero.
> Thank you,
> Tom Arnow
> Research Imaging Center,
> San Antonio, TX, USA
>
> /Users/martinez/fsl/bin/flirt -in /Users/martinez/Desktop/im2.hdr -ref
> /Users/martinez/Desktop/im1.hdr -out testimg -omat testimg.mat -bins
> 256
> -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof
> 6
> -interp trilinear
> WARNING::in calculating COG, total = 0.0
> Finished
>
> avwstats im1.hdr -R -r
> -228.000000 1086.000000 -23.016000 143.862000
> % avwstats im2.hdr -R -r
> -228.000000 1086.000000 -15.132000 141.234000
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