Mark,
I assume I cd to the folder then put in the message (this is what I have done)? Will it tell me when it is finished (it is taking a long time, but I assume that is because there are a lot of files)?
Thanks,
Emily
----- Original Message -----
From: Mark Jenkinson <[log in to unmask]>
Date: Friday, February 15, 2008 12:31 pm
Subject: Re: [FSL] reorientation
> Hi,
>
> There is no GUI option, but you can play about with fslswapdim on the
> command line to do it (run from the Terminal application). Just make
> sure you keep a backup of the original and do *not* keep any output
> where fslswapdim has printed a message about left/right flips, as this
> is quite dangerous.
>
> If you have a standard axial scan (that looks like the standard
> brain in
> orientation in fslview, except for being upside down in the
> sagittal and
> coronal views) then the following command should work:
>
> fslswapdim origdata -x y -z swappeddata
>
> All the best,
> Mark
>
>
>
> On 15 Feb 2008, at 16:46, Emily Stoneham wrote:
>
> > Hello!
> >
> > When I do an initial look at the functional images (289 to a
> > run), the sagittals are all upside down.
> > is there a way to fix all of them at once using the FSL GUI (I am
>
> > on a Mac)?
> >
> > Thanks,
> > Emily
> >
>
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