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ENH: Update from 28/12/2012 release

Matthew Webster requested to merge enh/JHU into master

This is an update of the JHU white matter labels using the 28/12/2012 update downloaded from:

http://www.loni.usc.edu/research/atlas_downloads

The header-implied orientation of the source files is incorrect as reported by

https://www.frontiersin.org/articles/10.3389/fnins.2013.00004/full

and verified by direct email from Susumu Mori.

The new atlas image was oriented to the existing version via the following:

fslswapdim ICBM_DTI_81_WMPM -x -y z ICBM_NIFTI_swap
flirt -in ICBM_NIFTI_swap -applyxfm -init $FSLDIR/etc/flirtsch/ident.mat -ref $FSLDIR/data/atlases/JHU/JHU-ICBM-labels-1mm  -out ICBM_NIFTI_1mm   -interp nearestneighbour
flirt -in ICBM_NIFTI_1mm -applyxfm -init $FSLDIR/etc/flirtsch/ident.mat -ref $FSLDIR/data/atlases/JHU-ICBM-labels-2mm -out ICBM_NIFTI_2mm -interp nearestneighbour

The only real difference in the update should be a region of voxels being relabelled from External Capsule (L/R) to Inferior fronto-occipital fasciculus (L/R). Note that the Uncinate fasciculus and Tapetum have different numerical designations, due to the addition of the Inferior fronto-occipital fasciculus labels.

Anatomical relabelling was additionally verified by Saad Jbabdi.

Edited by Matthew Webster

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