Dear Norm,
If your image is correctly labelled but you want to see it in the
same orientation as the MNI152 images, then you just need to
run one command:
fslswapdim invol RL PA IS outvol
and this will convert your image into the desired orientation.
Note that it may fail and tell you that you need to run the
command with LR rather than RL - if so, just do as it says.
Make sure you work with your original image though, and
not the output of your previous fslswapdim and fslorient
calls, as these may have erroneously changed the handedness
if you were not super-careful.
All the best,
Mark
On 20 May 2010, at 21:31, Norm L. wrote:
> To whom this may concern:
>
> I am also looking for information in regards to this old archive
> post from 2006 about FSLview orientation..
>
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;16I%2BUA;20060815074412%2B0100;ind06
>
>>
>> L L
>>
>> A TRA P S COR I
>>
>> R R
>>
>>
>> I
>>
>> A SAG P
>>
>> S
>>
>
> As shown above, I also get this problem when processing our T1 data
> and was wondering if there has been a fix for the current fslview
> 3.0.2, to force the displays to be displayed in its correct manner?
> -------------------
> These are the commands I used after using mri_convert .BRIK file -->
> nifti
>
> For T1s, we wanted to change it to radiological orientation.. so in
> my attempt, I tried:
>
> fslswapdim *data* x y z output_file
> fslorient -swaporient output_file
>
> where with the fslswapdim command:-x, -y, -z were done respectively.
>
> (See image in link: https://docs.google.com/leaf?id=0B_0SZVO9dXEoMjBkOTM5OWEtZTU3MS00NWM4LTg1OGMtNGNiYjYxMWUyMmYz&hl=en)
>
> This is what it gave me:
>
> when x+ = Y value INCREASED (neg to pos, moves through coronal slice
> from P-A)
> when y+ = Z value INCREASED (neg to pos, moves through axial slice
> from I-S)
> when z+ = X value DECREASED (neg to pos, moves through sag slice
> from neurological R-L)
>
> fslorient -getorient output_file = gives RADIOLOGICAL, although it
> is displayed in neurological format..swaporient again = will give
> neurological for '-getorient', but radiological orientation
> displayed.. if that makes any sense?
> --------------------
>
> Although, orientations are always correctly labeled, it would be
> awesome if I didn't have to turn my monitor in different ways in
> each orientation.
>
> Thanks for all your help,
> -Norman L.
>
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