Just to complete, the LGN mask in the FDT practical data comes from an in-house group LGN based on high res PD data courtesy of Holly Bridge.
Saad.
On 23 Jun 2011, at 13:09, Matt Glasser wrote:
> Well, if you use nonlinear registration to MNI, you can generally use the
> same subcortical ROIs across subjects, however such ROIs will be more
> variable with regard to the anatomy than correctly hand drawn ones (not
> less). I would put an ROI in the white matter posterior to the LGN and one
> at the beginning of the calcarine where the optic radiation is a clear "C"
> shape in coronal section on the color FA map.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Sean F Walsh
> Sent: Thursday, June 23, 2011 9:07 AM
> To: [log in to unmask]
> Subject: [FSL] Optic radiation tractography ROIs
>
> Dear FSLers,
>
> I would like to track the optic radiations in several subjects (about 80
> brains) and would appreciate some advice as to which regions of interest to
> use. I would like to automate the process as much as possible to avoid
> introducing too much variability with regards to the region of interests, in
> particular the placement of the ROI near the lateral geniculate nucleus. Of
> course this approach would only be as good as any registration that goes
> with it. I was considering using the part of the thalamic atlas which
> features projections to the occipital lobe as a seed point. This ROI however
> seems to be larger on one side than the other. I am worried that apart from
> introducing a left/right bias that I may also miss out on some parts of the
> tract which go to nearby parts of the thalamus.
>
> I know that in the fdt tutorial there is a lateral geniculate nucleus mask.
> Was this hand-drawn or taken from an atlas? If so, which one?
>
> Also are there any atlases available which feature V1 in each hemisphere, as
> in the tutorial example?
>
> Any recommendations will be warmly received,
>
> Many thanks,
>
> Sean
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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