Dear All,
I am trying to perform brain extraction on T1 3D images, however the dura appears too bright and thick compared to the underlying gray matter. It seems that I have a hard time stripping the dura away. Do you have any suggestions in terms of optimizing freesurfer parameters to help with this problem, or alternatively, do you suggest a specific T1 protocol (TE/TR) to dim the dura a bit? Thank you,
Octavian Lie.
Hi Octavian
what kind of scanner are you using? Andre van der Kouwe and Dylan Tisdall (ccd) have developed a multi-echo mprage that allows one to identify dura by it's short T2*. They might be able to give it to you depending on your scanner and relationship with Siemens. Otherwise it can be difficult, as lenghtening your TE to reduce the dura signal also reduced gray/white contrast.
cheers Bruce On Tue, 31 Jan 2012, octavian lie wrote:
Dear All,
I am trying to perform brain extraction on T1 3D images, however the dura appears too bright and thick compared to the underlying gray matter. It seems that I have a hard time stripping the dura away. Do you have any suggestions in terms of optimizing freesurfer parameters to help with this problem, or alternatively, do you suggest a specific T1 protocol (TE/TR) to dim the dura a bit? Thank you,
Octavian Lie. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Do you have a Siemens scanner?
You can compare your protocols with the examples at:
www.nmr.mgh.harvard.edu/~andre.
On Tue, 31 Jan 2012, Bruce Fischl wrote:
Hi Octavian
what kind of scanner are you using? Andre van der Kouwe and Dylan Tisdall (ccd) have developed a multi-echo mprage that allows one to identify dura by it's short T2*. They might be able to give it to you depending on your scanner and relationship with Siemens. Otherwise it can be difficult, as lenghtening your TE to reduce the dura signal also reduced gray/white contrast.
cheers Bruce On Tue, 31 Jan 2012, octavian lie wrote:
Dear All,
I am trying to perform brain extraction on T1 3D images, however the dura appears too bright and thick compared to the underlying gray matter. It seems that I have a hard time stripping the dura away. Do you have any suggestions in terms of optimizing freesurfer parameters to help with this problem, or alternatively, do you suggest a specific T1 protocol (TE/TR) to dim the dura a bit? Thank you,
Octavian Lie. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Andre van der Kouwe -
Bruce Fischl -
octavian lie