Dear SPMers,
Although this is not strictly an SPM question, as people have previously
mentioned the use of AIR to reorient images I am hoping that someone might
be able to help me with a problem I am having.
My images are acquired coronally and each volume is comprised of 30 slices
(posterior to anterior) and each slice has dimensions 64 x 64 (voxel
dimensions 3 x 3 x 6). When I use MRIcro to split the raw data into its
separate volumes and create a .hdr file, MRIcro reorients the images into
an axial orientation which SPM expects. However, this now means that SPM
sees the Z dimension as 64 rather than 30 and therefore I cannot perform
slice timing as SPM expects a wrong 64 slices.
After reading several previous messages from people with the same problem I
decided to use AIR to reorient my images so that I could interchange the ZY
axis to allow me to do slice timing. The problem is that when I rotate my
images using AIR the image intensities become completely distorted when
viewing them in SPM (see attached picture). When I looked at the header
information in AIR I noticed that global max for the original image was 255
and for the rotated image was 65535. After reading the AIR website I
thought that the problem was perhaps that it was loading the images as 8
bit images and then converting them to 16bit images during reorienting.
However this was not the case after trying the same process using the 8bit
version of AIR which made the images even worse after reorienting.
I have also tried saving the volumes in MRIcro as ‘axial’ rather than
coronal right so that they are in the right orientation to do slice timing
and then reorienting them in AIR afterwards into the axial plane for
normalization, but this has a similar effect.
If anyone has any idea what I may be doing wrong, any help would be greatly
appreciated.
With thanks in advance
Jenny Bell
PhD Student - University of Nottingham
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