Mark, when you say 'use the right filenames' how do I put those in the command? Also, do I list all of them, or is the folder name sufficient?
----- Original Message -----
From: Mark Jenkinson <[log in to unmask]>
Date: Friday, February 15, 2008 1:14 pm
Subject: Re: [FSL] reorientation
> Hi,
>
> Yes, cd into the directory then type the command I said (using the
> right filenames for your data).
> It should not take very long even with a big dataset (lots of
> timepoints).
> If it is taking more than 5 minutes then something has probably
> gone
> wrong.
> Of course the time can depend on the speed of your machine/network/
> disk storage and how
> many users are doing things.
> It will not print any special message though when it works.
> It will simply give you a fresh prompt (like cd would do).
>
> All the best,
> Mark
>
>
>
> On 15 Feb 2008, at 18:08, Emily T Stoneham wrote:
>
> > 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
> >>>
> >>
> >> <estoneha.vcf>
>
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