Hi - it sounds like maybe you are taking a rotation matrix appropriate for
the structural and applying it to the functional - given that they
probably have different FOV it isn't appropriate to do that - derive a new
matrix for the functional (although it's easiest to follow Mark's first
suggestion and just use avwswapdim on the images directly).
Thanks, Steve.
On Tue, 26 Nov 2002, Jimmy Jensen wrote:
> Hi Mark,
> Thanks for your quick reply. I have tried your suggestions and it works
> fine for my anatomical image. However, my functional is still not
> working properly. When using slices on the transformed image it is
> partly "out of the picture" if you know what I mean. It is only a
> partial volume (15 slices x 4mm), but I guess that should not make any
> difference?
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Mark Jenkinson
> Sent: Tuesday, November 26, 2002 4:00 PM
> To: [log in to unmask]
> Subject: Re: [FSL] rotate image
>
> Hi Jimmy,
>
> If you only want 90 degree rotations I suggest using avwswapdim instead.
> By the look of your matrix you just need to do:
> avwswapdim inputimage x -z y outputimage
>
> If you leave off the last argument (outputimage) then you'll see the
> transformation matrix that it generates, with the appropriate FOV.
> You could then save this matrix and apply it with flirt as per usual
> (or use the new ApplyXFM gui).
>
> All the best,
> Mark
>
>
>
>
> On Wednesday, November 27, 2002, at 07:02 AM, Jimmy Jensen wrote:
>
> > Dear FSL,
> > I am trying to rotate an image 90 degrees in pitch using flirt but it
> does
> > not look so good. I have tried: flirt -in image -out newimage
> -applyxfm -
> > init matrix -ref image. I have tried it with several versions of
> > transformation matrices like:
> > 1 0 0 0
> > 0 0 -1 0
> > 0 1 0 0
> > 0 0 0 1
> >
> > I have also used the FOV in the fourth column but it did not help me.
> Any
> > suggestions where I am doing wrong wold be appreciated.
> >
> > Thanks
> > Jimmy
> >
> > --------------------------------------------
> > Jimmy Jensen, PhD
> > PET centre
> > Centre for Addiction and Mental Health
> > Clarke Division
> > 250 College St.
> > Toronto, ON, M5T 1R8
> >
> > Phone (416) 535-8501 ext. 6280
> > Fax (416) 979-4656
>
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
|