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
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:
- 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Lukas.Scheef＠ukb.uni-bonn.de -
Matt Glasser