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
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