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After unwarping oblique EPI images with ppge AFNI briks came out up side down. How can I prevent this?

April 26, 2017afni briks came epi images oblique ppge

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After unwarping oblique EPI images with ppge AFNI briks came out up side down. How can I prevent this?

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This problem occurs because the bxh tools that convert data to an intermediate format (ANALYZE) can not handle correctly oblique slice stacks that are acquired in the S-I direction. (NOTE: ppge2 does not use bxh tools and should therefore get around this issue). In that case the conversion results in the following error message: Converting bxh to ANALYZE WARNING: not a supported Analyze orientation — labeling as transverse unflipped (0) anyway… The flipping of the oblique slices (rotated along the axis perpendicular to saggital plane) can be prevented by the following slice prescription procedures: –rotating slices counterclockwise (slice angle > 180 deg) and dragging mouse UPWARD to add slices. –rotating slices clockwise (angle <180 deg) and dragging DOWN to add slices. In either case the resulting slice stack is numbered bottom-up, and does not confuse ppge.