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" <fis...@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.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 >> >> >>_______________________________________________ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it >is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in >error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
