Hi Buyean,
> can one use SPM5 Display to reorient the image (Nifti) for FSL
SPM5's reorientations get written to the NIfTI headers, so you could
use FLIRT's -usesqform option to resample the reoriented images as
Mark describes here:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=fsl&P=40969
However, I think Steve made the point that you should probably avoid
the interpolation errors from such reorientation and resampling, by
instead using only fslswapdim. As you said, it is limited to 90 degree
rotations, but those have the benefit of being exact -- no
interpolation is needed. Hopefully if you get the orientation correct
to the nearest 90 degrees then the flirt calls within sienax should be
successful. If not, you might be able to modify the sienax script to
make use of the usesqform FLIRT option internally, but I haven't
looked into that... (I hope this isn't the third idiotic email I've
sent to this list recently... ;-))
Note that manual reorientation is more important in SPM5 than in FSL,
because at present the unified segmentation model in SPM5 doesn't
model non-brain tissue very well, so its affine registration step
needs a good rigid initialisation to succeed. (There are a few posts
by John Ashburner on the SPM list with similar wording.) FLIRT on the
other hand, uses a simpler, more general cost function, with a more
sophisticated and robust optimisation routine (described in the tech
reports, and the course slides last time I looked), which generally
seems to be very good. In fact, I once played around with using FLIRT
to generate the initial transformations for SPM5; this seemed to work
well if the subjects can be successfully registered to MNI using rigid
registration only, but gets complicated if you have to enable scaling
for FLIRT to work well.
Anyway, I'll stop waffling.
Best,
Ged
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