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 ---28.03.2013 15:37:47---Matt Glasser <matt@ma-tea.com>

Matt Glasser <matt@ma-tea.com>  28.03.2013 15:37

An 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
>
>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.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:
>>
>> 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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