No.
If you know scripting you can do it with a little script.
Otherwise, just run it one at a time.
Make doubly sure that you backup and check that the first result
is OK before doing the rest though, as otherwise it is a great waste!
All the best,
Mark
On 15 Feb 2008, at 18:26, Emily T Stoneham wrote:
> 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>
>>
>> <estoneha.vcf>
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