You can use fslswapdim to correct this problem. There are the three axes x,
y, and z which you can negate to flip the image across the axis. You can
also reorder x y and z to change how the data is sliced. If the utility
gives you a warning "changing left-right orientation" you can use -x (or
take that away if you were using it previously). I would try something like
y z x to see if that puts the correct plane of section in the correct view,
and then use minuses as needed to correct upsidown or backwards images.
After doing this you might also have to use fslorient -deleteorient to get
the labels to display correctly. The first time you use this on a dataset
you need to be very sure left and right are where you think they are, and
then you can use whatever procedure works so long as the original data is
always in the same orientation.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Anastasia Ford
Sent: Thursday, March 20, 2008 1:48 PM
To: [log in to unmask]
Subject: [FSL] FSLview image orientation
Hello FSL experts,
Im having trouble displaying my T1 image from the Phillips Achieva scanner
in FSLview. Images are stored in AFNIs BRIK/HEAD format and I converted them
both to Nifti and to Analyze. When I open either one in FSLiview the axial
view displays an upside-down sagittal image, coronal view displays a 90
degree rotated axial, and sagittal view displays 90 degree rotated coronal
image. Do you have suggestions on how to fix this problem?
Thank you
Anastasia
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