Dear Mark,
Thanks for your reply. I had another go at registration of reoriented images and it worked!!!!
I guesss now all I need to do is to apply that to the rest of my images and re-do the segmentation.
With reference to he problem I had I'd like to ask few questions:
Does fslreorient2std change my images-do I get the same ''volume'' back?
I'm still not quite sure why 11 of my sagittal images were fine but 9 were a bit dodgy. Was the registation problem due to the orientation of my images or was it something else?
Should I re-do my segementation on the entire sagittal data set (with preprocessing using flsreorient2std on all sagittal data) for sake of consistency in my results.
cheers,
Lukasz
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