What do you mean by "not well oriented while looking at them in fslview"?
Is the brain just sideways or upside-down in the display, or are the
orientation labels shown within fslview actually in the wrong position?
You might want to read #7 in the FSL FAQ, which makes clear that using
fslswapdim in the fashion that you appear to be doing (i.e., without
fslorient) will mess up the orientation if you are starting with a valid
nifti file (i.e., one in the which the R/L, A/P, and S/I labels show up in
the proper locations within fslview).
Best,
-MH
> Hi,
>
> I am using feat to run analyses on fMRI data that were acquired sagittally
> (anatomical and EPI runs).
>
> Because of the direction of the acquisitions, the nifti files created from
> the dicom with dcm2nii were not well oriented while looking at them in
> fslview and the registration step did not work properly (everything was
> flipped 180°. The frontal lobe of the example_function was in the
> occipital
> of the standard images etc...).
>
> I then decided to re-orient the nifti files using:
> fslswapdim input.nii.gz -z -x y output.nii.gz
> But in doing this I am afraid it might be problematic for the slice timing
> correction step. Am I right? How does feat determine the slice order and
> the
> direction of slice acquisition?
>
> So as an other solution I kept the run and anatomical we acquired in the
> "wrong orientation" and created an icbm152 template (using fslswapdim -y z
> -x) with the same orientation as our acquisitions. This way, the
> registration seems to work properly and I could run a group analysis.
> My only concern is about the coordinates of my images. Does fslswapdim
> affect the coordinates of the volume acquired? Are the coordinates of the
> cluster list still accurate (as I used a template with different
> orientations)?
> If I reorient my final group statistic maps in the "right" orientation
> using
> once again fslswapdim (-z -x y), can I use the Atlas tools without having
> to
> worry about the coordinates?
>
> I went through a lot of anterior posts in the FSL archives. That is how I
> discovered fslswapdim (thank you for those very useful posts!). I did not
> find any post regarding analysis of data acquired sagittally though (maybe
> I
> did not use the right keywords...).
> Any help and suggestions will be very welcome.
>
> Thanks in advance!
> Best,
>
> Cécile Madjar
>
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