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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