Dear Cinly,
After the first-level analysis the copes and varcopes are still in
the native space and so will match whatever the input images
are in terms of space and "orientation". At the start of higher-level
analysis everything is resampled in standard space where things
match the MNI152 space and orientation.
Note that FSL has been able to cope with mixed radiological/neurological
pipelines for several years now, so you should be able to continue
with all your analyses without worrying about what "orientation" any
of the images are in anyway.
I hope this answers your questions.
All the best,
Mark
On 1 Jun 2011, at 12:16, Cinly Ooi wrote:
> Dear All,
>
> Sorry for bothering you all about question with orientation.
>
> I performed a lot of FEAT analysis and due to a mix up, my input files are a mixture of radiological/neurological format.
>
> In the .fsf file, I used
>
> set fmri(regstandard) "/path/to/fsl/data/standard/MNI152_T1_2mm.brain"
>
> Now I have to extract statistics using a mask.
>
> My question is: after applying
>
> featregapply my.feat
>
> what is the orientation (Neurological/Radiological) of my copeX.nii and varcopeX.nii data in my.feat/reg_standard/stats/ without reading their sform_code/qform_code value?
>
> Needless to say I was hoping that those files are in a specific orientation after standard space registration regardless of the orientation of the original fMRI images. ;-)
>
> Many thanks in advance and Best Regards,
> Cinly
>
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