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
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