FSL users,
I am processing some structural data gathered from multiple sites using multiple scanners. Some of the images display in normal convention within fslview, while others do not. The directional information is maintained (i.e. anterior is correctly labeled), but the display is off. Using fslreorient2std does not correct this problem. If another image viewer is used such as freeview, all of the images are displayed with similar orientations. I converted the images initially using dcm2nii and tried with and without the -reorient option. I also used the more updated dcm2niix with the same results. Doesn't seem tied to specific scanners as 3T Trio data from our site displays normally while 3T Trio data from another displays with the abnormal orientation.
Has anyone else hit this problem? Screenshots of what I am "abnormal" as well as a "normal" orientation with freeview are available from the link as is a problematic nifti image. We are trying to implement some automated screen capturing as part of a QC process so this has throw a wrench in the process. Any help would be appreciated.
https://wustl.box.com/s/vmwi7g443u00t9gtq4qne0ymdpurlvzm
Brian
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