On Mon, Jan 28, 2013 at 9:14 AM, Dr. András Jakab <
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> Dear Gabor,
>
> I think it strongly depends on what you are trying to do, i.e. connectivity
> based subdivisions are not the same as nuclei or nuclei groups, they just
> very roughly overlap.
>
> Our practice here is:
>
> 1. All probtrackx calculations are performed using non-linear (FNIRT)
> transformations to and from the subjects space to - from MNI, like it is
> described in the FNIRT manual. With this approach it is very straightforward
> to use masks of the cortical regions for classification targets
> (somatomotor, premotor, sensory, temporal, occipital, etc.)
>
> 2. We have a standard space, high resolution Thalamus Atlas (based on the
> Morel's atlas of the human thalamus and basal ganglia). The original, shape
> model-based mesh atlas was "voxelized", so you can use each
> (histology-based, population averaged) nuclei in the standard space as
> volumetric labelled maps. For this you should contact me and the ETH in
> Zürich to get free license.
>
> For the reproducility and intersubject variability:
> Traynor, C., Heckemann, R. A., Hammers, A., O’Muircheartaigh, J., Crum, W.
> R., Barker, G. J., & Richardson, M. P. (2010). Reproducibility of thalamic
> segmentation based on probabilistic tractography. NeuroImage, 52(1), 69–85.
>
> Hope this helps.
> András
>
>
> On Mon, Jan 28, 2013 at 3:02 PM, Gabor Perlaki <
[log in to unmask]>
> wrote:
>>
>> Dear all,
>>
>> I'd like to measure some MR parameters in the thalamic nuclei. It is very
>> laborious to draw cortical masks for the thalamic segmentation in each
>> subject separately, so I am thinking in 2 options:
>>
>> 1, Using the thalamic connectivity atlas provided by FSL and register the
>> nuclei maks into subject space.
>>
>> 2, Using cortical masks drawn in MNI space and register them into subject
>> space for connectivity based thalamus segmentation.
>>
>> Are they usable options?
>> Regarding the first option, is it accurate enough to use the registered
>> standard space atlas masks for this purpose, or are there very big variation
>> in the location of thalamic nuclei between subjects?
>>
>> Thanks,
>> Gabor
>
>
>
>
> --
> Andras Jakab, M.D. Ph.D.
> Post Doctoral Researcher
> Dept. of BioMedical Laboratory and Imaging Science
> Faculty of Medicine, University of Debrecen
> 98. Nagyerdei Krt.
> 4032 Debrecen
> Hungary
> Phone:
+3652255170
> Cellular:
+36305095083