Hi,
I agree with Markus.
What fslswapdim will try to do is to move the labels with the image, so
that if it is being re-oriented for viewing based on the labels then you
will not see any difference. If you view with FSLView then you will
see the direct data orientation (which you are changing) as well as
the labels (which will shift with the data - except see below).
Also, you need to be very careful using "x z y" as it is changing the
handedness of your coordinate system (flipping left/right orientation)!
This can have disasterous effects for keeping track of left and right in
your image, as the labels will not be changed in this case. I recommend
using "-x z y" if x is your left-right direction, so that you maintain
your coordinate left/right orientation but still swap the axes. Be
very careful about the warnings that fslswapdim issues.
All the best,
Mark
On 6 Feb 2009, at 08:45, Markus Gschwind wrote:
> Hi!
>
> Be VERY careful with looking at images with MRIcroN!
>
> 1. Be sure that you have NOT checked the *Reorient (reslice) image
> when loading* box under Help>Preferences, which is normally checked
> by default
>
> 2. Be sure that you know which side is what (*flip L/R* under View).
>
> Otherwise, you will go through hell! And even more when you use
> ANALYZE files ;-)
>
> Cheers,
> Markus
>
>
>
>
>
> 2009/2/6 dfwang <[log in to unmask]>
> Hi, Mark,
>
> I viewed the results with MriCron. I will check it again with FSLview.
>
> Thanks a lot.
> Richard
> ----- Original Message ----- From: "Mark Jenkinson" <[log in to unmask]
> >
> To: <[log in to unmask]>
> Sent: Thursday, February 05, 2009 7:01 PM
> Subject: Re: [FSL] fslswapdim does not work properly
>
>
>
> Hi,
>
> It works here.
> How are you checking whether it works?
> Are you looking with FSLView?
>
> All the best,
> Mark
>
>
>
> dfwang wrote:
> Dear FSLers,
>
> I found that the following command
>
> fslswapdim input.nii.gz x z y output.nii.gz
>
> does not work properly. That is, the y and z dimension doe dot
> exchange.
>
> Any comments for this problem is welcome!
>
> Best wishes,
> Richard
>
>
>
>
> --
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
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