1a) You would do this after running recon-all on the T1-weighted image. It
will only adjust the surfaces, not the segmentation. Something like
recon-all -T2pial <path to flair>
1b) this will work with either, but in my experience the FLAIR helps more
to distinguish dura from gm
2) Yes. The standard aseg will label them and we have some custom tools
that are more accurate if you have other image contrasts. I don't think
they are quite distributed yet, but perhaps Doug can comment.
3) Sure, this isn't too hard. David Salat has published using the
gray/white ratio as an interesting biomarker and the techniques would be
pretty similar. I think Matt mostly used FreeSurfer for his analysis, but
perhaps he can comment on the particulars
cheers
Bruce
On Thu, 28 Mar 2013, lukas.sch...@ukb.uni-bonn.de wrote:
Hi FreeSurfer experts!
We have isotropic T1/T2 and FLAIR volumes for a larger cohort. It would be
fine to use the T2 / FLAIR volumes to improve the segmentation and to
perform a couple additional analyses using FS. This leads to the following
questions:
1) How do I incorporate T2/Flair volumes into the recon all processing
stream?
a) Would it be like: recon-all bert -all -T2 /luke/xyz/007-T2.nii ?
b) What is expected to get the better results regarding the pial surface:
FLAIR or T2? (both are at 1x1x1mm)
2) Is there any module in FS to detect white matter lesions?
3) How can I perform myelin mapping using the ratio method (T1w/T2w)? Or do
I have to switch to Caret?
Many thanks in advance for your help and advice!
Best wishes,
Luke
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