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Bug 83 - flipped volume in ft_volumesegment

Status	CLOSED FIXED
Reported	2010-05-19 11:33:00 +0200
Modified	2011-01-12 14:37:37 +0100
Product:	FieldTrip
Component:	core
Version:	unspecified
Hardware:	PC
Operating System:	Mac OS
Importance:	P5 normal
Assigned to:	Jan-Mathijs Schoffelen
URL:
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Jan-Mathijs Schoffelen - 2010-05-19 11:33:11 +0200

The voxel-data in the output to ft_volumesegment often appears to be flipped (at least for .mri mris in the input). Investigate whether this is input mri specific. Investigate what causes it, and fix. The current situation makes it necessary to do flipdim(flipdim(flipdim...,3),2),1) for all of the segmented volumes.

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Jan-Mathijs Schoffelen - 2011-01-06 11:32:53 +0100

the flipping issue is introduced by the call to align_ijk2xyz. Essentially, the volumes need to be unflipped after segmentation in order for them to end up in the correct orientation with respect to the output anatomy. This has been fixed by changing ft_volumesegment and align_ijk2xyz. @Arjen: this is related to bug 350. Could you check whether there is now a good alignment between the segmented volumes and the anatomy without flipping?