Ahhh! I get it :) so, there is no way to do this for all files at one time, then?
Emily
----- Original Message -----
From: Mark Jenkinson <[log in to unmask]>
Date: Friday, February 15, 2008 1:26 pm
Subject: Re: [FSL] reorientation
> Hi,
>
> You need to run this command once (separately) for every image,
> either structural or functional, that you want to change.
> Remember to make a backup first!
>
> The filenames are in the command.
> I put in the "origdata" and "swappeddata" as examples.
>
> If you have an image file called "functional_run2.nii.gz" and
> you want to change its orientation (stop it being upside down)
> then you would run:
>
> fslswapdim functional_run2 -x y -z functional_run2_swapped
>
> to create a new image file called "functional_run2_swapped.nii.gz".
> You can use whatever names you like though.
>
> Make sure you look at the output in fslview to see if it has worked
> before doing this to any other files.
>
> All the best,
> Mark
>
>
>
> On 15 Feb 2008, at 18:19, Emily T Stoneham wrote:
>
> > 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>
> >>
> >> <estoneha.vcf>
>
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