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Hi, This turns out to only be a problem for the FAST boundary correction method when applied to neurologically-ordered images. It is easy to fix in the first_boundary_correction script, and the fixed version can be downloaded from: http://www.fmrib.ox.ac.uk/fsldownloads/patches/first_boundary_corr Just download this and copy it into $FSLDIR/bin/ on your machine (replacing the old one) and everything should work fine. All the best, Mark On 11 Aug 2009, at 01:45, Buyean Lee wrote: > Hi, > > FSL: version 4.1.4 > Tool: FIRST. > > I found that many boundary-corrected ROIs (in > *_all_fast_firstseg.nii) are not registered to the originally > segmented ROIs (in *_all_fast_orisegs.nii); see below for the list. > > In contrast, the boundary-corrected ROIs generated with an old > version (FSL 4.1.2) are correctly registered to the original ROIs. > > Let me know where I need to check to fix this error. > > Thank you, > > Buyean > > 4 Left-Lateral-Ventricle - wrong > 10 Left-Thalamus-Proper - correct > 11 Left-Caudate - wrong > 12 Left-Putamen - correct > 13 Left-Pallidum - correct > 16 Brain-Stem /4th Ventricle – left-right flipped > 17 Left-Hip pocampus - wrong > 18 Left-Amygdala - wrong > 26 Left-Accumbens-area - wrong > 43 Right-Lateral-Ventricle - wrong > 49 Right-Thalamus-Proper - correct > 50 Right-Caudate - wrong > 51 Right-Putamen - correct > 52 Right-Pallidum - correct > 53 Right-Hippocampus - wrong > 54 Right-Amygdala - wrong > 58 Right-Accumbens-area - wrong