Hello Yaroslav,
We hope to be making a patch release of FSLview ( including the updated H-O atlas ) in the next few days!
Kind Regards
Matthew
> Are there any estimates on ETA of such a lovely patch release?
>
> Thanks in advance!
>
> On Thu, 10 Jan 2013, Stephen Smith wrote:
>
>> Hilarious! Yes this has been solved now internally - I think we're just
>> about ready to release a patch on the atlas (and I believe an added bonus
>> - a nonlinear version of H-O too).
>> Cheers.
>> On 10 Jan 2013, at 13:55, Yaroslav Halchenko wrote:
>
>> 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
>
>> [1]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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