Hi,
We recently spoke with someone doing fMRI analysis with FSL and they ran
into some issues with finding that using fslswapdim and fslorient was
actually flipping their data such that right was left and left was right
(the functional header said it was in neurologic orientation and the
structural said radiologic; when he swapped only the functional images,
the functional and structural became mirror images of each other). I
believe he heard from someone on the FSL list who mentioned that the
procedures for dealing with orientation have changed recently, and that he
no longer needs to use fslswapdim (and maybe fslorient, too?).
So here are our questions: Was there really a change in how orientation
is dealt with, and if so, does it affect all types of images (fMRI,
structural, DTI, etc.)? Do we need to still run fslorient or is it just
fslswap that should not be used? If orientation procedures have indeed
changed, when did this change take effect? And finally, at what stage do
the changes apply, i.e. was there a change at the stage of unpacking or
is the change further downstream (I'm asking this because we did some
recent processing of images that were unpacked awhile ago, so they may
not be affected by this change and would still need to be swapped--I
think).
Our current questions are specifically about DTI analysis, but we will
also be using FSL for fMRI in the near future. We are currently using both
bedpostx/probtrackx and randomise for the DTI analyses. Also, we are using
unpacksdcmdir to unpack our images. We are using NIFTI format images.
Thank you!
Sandra Woodman
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