Thanks for comment!
I have some more questions to ask.
I registered DTI data to MNI space (by registration).
1) If I want to use label files for seed masks, Aren't they supposed to be in same space? (like MNI...)
No they can also be in "FreeSurfer space" - there are instructions on how to do that on the FSL wiki.
2) If they are, how can I do that?
Seed (1).
and one more thing,
3) Can I use just label files only for seed masks? or should I preprocess images with freesurfer (recon1, 2, 3)?
You need to run recon_all (not sure if 2 or 3) to get the label files, then you can use these label files in label2surf to create seed masks for probtrackx2.
Cheers
Saad
Thanks,
YM Huh
2013/2/5 Saad Jbabdi
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Hi
On 5 Feb 2013, at 09:26, YM Huh wrote:
> Dear experts,
>
> I ran DTI images Bedpostx and registering, and now trying whole-brain probabilistic tractography.
>
> What i'm gong to do is to 1)make seed masks with freesurfer label files, and 2)perform tractography with multiple mask mode and get seed*seed matrix.
>
> I found comments from other post saying that I must first transform label files into a surface file, using the label2surf command.
>
> 1)will this process make label files to be in MNI152 space?
No.
>
> 2)and which label should I use? (There are a few labels for freesurfer.)
It depends what seed masks you want to use. Each label file produced by freesurfer's recon_all is a cortical region.
>
> 3)And I wonder if there is better cortical parcellation scheme for whole brain tractography.
It would be nice if there was one.... Still an open research area!
Cheers
Saad
>
> Thanks,
>
>
> YM Huh
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
