Actually, I would argue that it is VERY difficult to track from the
chiasm to V1. if you want to define the optic tract you may not be able
to with axially aquired data if your slice thickness is too large or
have gaps. as far as the optic radiata go. you may need to use symmetric
masks in the anterior optic radiation and V1. look at
Underdevelopment of Optic Radiation in Children With Amblyopia: A
Tractography Study.
American Journal of Ophthalmology, Volume 143, Issue 4, Pages 642-646
S. Xie, G. Gong, J. Xiao, J. Ye, H. Liu, X. Gan, Z. Jiang, X. Jiang
or
Between session reproducibility and between subject variability of
diffusion MR and tractography measures
Neuroimage, Volume 33, Issue 3, 15 November 2006, Pages 867-877
E. Heiervang, T.E.J. Behrens, C.E. Mackayc, M.D. Robsonc and H.
Johansen-Berga
cheers
Scott
Tim Behrens wrote:
> Hi - if you can't see the optic tract by placing a seed in the tract
> and visualising the output, then there is something wrong with your data.
>
> The first thing to do is just to use single seedmask mode to see if
> you can visualise the tracts. If you can't see anything in this mode,
> you need to go back to your data.
>
> The most likely problem is your bvectors being wrong. You should check
> dti_v1 in lines mode. The lines should make continuous pathways in
> all 3 planes.
>
> If they do, you should check whether your data is neurologically
> oriented (fslorient -getorient)- if this is the case there are a few
> problems to overcome but it is do-able. We can walk you through it.
>
> If everything looks good and your data is radiological but you still
> can't see the major pathways, you can stick the data on out upload and
> someone will take a look over the next few days
>
> www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>
> Cheers
>
> T
>
>
>
>
> On 24 Feb 2008, at 01:04, Anastasia Ford wrote:
>
>> Matt and FSL experts,
>>
>> I will try to run the probtrackx from the command line using your
>> suggestion.
>> I also tried mapping the optic tract by using a single mask of the optic
>> chiasm and the resulting tracks do not look correct. None of them even
>> reach the occipital cortex, and very few reach LGN. Are thre any general
>> guidelines for tract mapping in terms of mask seeds? For example,
>> should I
>> always try to use the symmetric approach you mentioned, or use one mask
>> that would contain say the chiasm, LGN, and the visual cortex?
>> Im really struggling with what options to choose and very few of my
>> tracks
>> come out correct. I would appreciate if someone could walk me trough the
>> mapping process of one prominent tract (how many masks, wapoints,
>> exclusion masks).
>>
>> I appreciate your help,
>>
>> Anastasia
>>
--
========================
Scott Kolbe
Postgraduate Student
Neuroimaging Group
Howard Florey Institute &
Centre for Neuroscience
University of Melbourne
VIC, Australia, 3010.
ph: +61 3 8344 1887
email: [log in to unmask]
website: http://www.neuroimaging.org.au/index.php?id=383
