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>
|