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As far as I know they are fine, yes. Cheers. On 10 Jan 2013, at 14:17, Marenco, Stefano (NIH/NIMH) [E] wrote: > The paper that you cite makes me ask: are the JHU atlases used for tractography and for white matter labels obtained through the FSL distribution in the correct R-L orientation and labeled appropriately? > > Stefano Marenco, MD > NIMH/CBDB > 10 Center Drive, Bldg 10 room 3C103 > Bethesda MD 20892 > Tel 301 435-8964 > Fax 301 480-7795 > Email: [log in to unmask] > > > -----Original Message----- > From: Yaroslav Halchenko [mailto:[log in to unmask]] > Sent: Thursday, January 10, 2013 12:55 PM > To: [log in to unmask] > Subject: Re: [FSL] Incorrect probabilities in Harvard-Oxford-sub Left hemisphere > > NB a regular friendly monthly buzzzzz > > is anyone interested to do bits more of reverse-engineering > analysis and co-author a little paper similar to > > http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2013.00004/full > Torsten Rohlfing > Incorrect ICBM-DTI-81 Atlas Orientation and White Matter Labels > > ;-) > > > On Tue, 04 Dec 2012, Yaroslav Halchenko wrote: > >> and just to keep things at least somewhat luke warm (thus cooking), here >> is another visualization summarizing the problem. > >> I took left hemisphere, mirrored right hemisphere (so more or less now they >> should be 'corresponding'), resorted areas from what they were in atlas >> so they are in correspondence as well > >> for each voxel in each of the two hemispheres: >> - computed 'max probability' area for each voxel and assigned index >> from >> new index old index area >> 0, 7, 'Brain-Stem')), >> 1, 10, 'Left Accumbens')), >> 2, 9, 'Left Amygdala')), >> 3, 4, 'Left Caudate')), >> 4, 1, 'Left Cerebral Cortex ')), >> 5, 0, 'Left Cerebral White Matter')), >> 6, 8, 'Left Hippocampus')), >> 7, 2, 'Left Lateral Ventrical')), >> 8, 6, 'Left Pallidum')), >> 9, 5, 'Left Putamen')), >> 10, 3, 'Left Thalamus')) > >> - added %probability/100 to each index, so e.g. value of >> 4.67 is "Cerebral Cortex" at 67% > >> scatter plot left hemisphere against right flipped: >> http://www.onerussian.com/tmp/test-left+right_rev.png > >> you can easily see that while some areas seems to be Ok (e.g. brainstem ;) ) >> others "leak" too heavily among each other, and "right" probabilities >> tend to be generally higher than left for each one of those areas > >> On Wed, 07 Nov 2012, Yaroslav Halchenko wrote: > >>> On Wed, 31 Oct 2012, Yaroslav Halchenko wrote: >>>> On Wed, 31 Oct 2012, Stephen Smith wrote: >>>>> Hi Yaro - thanks for letting us know. We'll look into this ASAP and >>>>> update this if necessary. >>>> Great -- thanks in advance! > >>> And while you are at it, might be worth fixing a spelling typo in the >>> <type> of those: > >>> /usr/share/fsl/data/atlases/Cerebellum_MNIflirt.xml: <type>Probabalistic</type> >>> /usr/share/fsl/data/atlases/Cerebellum_MNIfnirt.xml: <type>Probabalistic</type> >>> /usr/share/fsl/data/atlases/HarvardOxford-Cortical.xml: <type>Probabalistic</type> >>> /usr/share/fsl/data/atlases/HarvardOxford-Subcortical.xml: <type>Probabalistic</type> >>> /usr/share/fsl/data/atlases/JHU-tracts.xml: <type>Probabalistic</type> >>> /usr/share/fsl/data/atlases/Juelich.xml: <type>Probabalistic</type> >>> /usr/share/fsl/data/atlases/MNI.xml: <type>Probabalistic</type> >>> /usr/share/fsl/data/atlases/Thalamus.xml: <type>Probabalistic</type> > -- > Yaroslav O. Halchenko > Postdoctoral Fellow, Department of Psychological and Brain Sciences > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 > WWW: http://www.linkedin.com/in/yarik --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------