Dear Matt!
Thanks a lot. We do have both FLAIR and T2 -> so I could use the FLAIR for the clean-up procedure and use the T2 volumes for myelin part...
Best wishes,
Luke
Matt Glasser matt@ma-tea.com An 28.03.2013 15:37 Bruce Fischl fischl@nmr.mgh.harvard.edu, Lukas.Scheef@ukb.uni-bonn.de Kopie freesurfer@nmr.mgh.harvard.edu Thema Re: [Freesurfer] Incorporating (high resolution) T2- and FLAIR volumes
I find the T2w image works well for removing dura and blood vessels, but I'm not sure FLAIR would work for T1w/T2w myelin mapping because of what would happen to the ratio near the pial surface.
Instructions for T1w/T2w myelin mapping are available here: http://brainvis.wustl.edu/wiki/index.php/Caret:MyelinMaps
One starts with FreeSurfer outputs.
Bruce: do you guys have an unsmoothed group average grey/white map? We could do a quick comparison on fsaverage if you guys were interested.
Peace,
Matt.
On 3/28/13 7:45 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
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
- 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.
- 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.Scheef@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:
- 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)
Is there any module in FS to detect white matter lesions?
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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