Hello, We are starting to use FreeSurfer v4.5.0 for segmentation purposes and after running freesurfer and correcting the wm surfaces following the online instructions we still get abnormal surfaces (wm looks better after corrections, but gray matter still the same). We are suspecting the problem to be due to intensity problem in the original T1-weighted volumes and thus we would like to consult with you the T1 sequence we use to know if there is what we could fix/change about that.
T1-weighted scans were imaged using 3D FSPGR BRAVO sequence (TR 12.1ms, TE 5.2 ms, slice thickness 1.0 mm, FOV 24.0 cm, matrix 256 x 256, and flip angle 20 º, parallel imaging factor 2, NEX 1).
Thanks a lot in advance, Ahmed
Hi Ahmed,
The TR is quite short and the TE is probably too long. Ideally we use mprage if we can, but if it's SPGR we try to minimize the TE (ideally 2ms or less) and use a TR of around 20ms, and a somewhat bigger flip angle, maybe 30deg. What coil are you using and what field strength?
cheers Bruce
On Wed, 30 Jun 2010, Ahmed Abou Elseoud wrote:
Hello, We are starting to use FreeSurfer v4.5.0 for segmentation purposes and after running freesurfer and correcting the wm surfaces following the online instructions we still get abnormal surfaces (wm looks better after corrections, but gray matter still the same). We are suspecting the problem to be due to intensity problem in the original T1-weighted volumes and thus we would like to consult with you the T1 sequence we use to know if there is what we could fix/change about that.
T1-weighted scans were imaged using 3D FSPGR BRAVO sequence (TR 12.1ms, TE 5.2 ms, slice thickness 1.0 mm, FOV 24.0 cm, matrix 256 x 256, and flip angle 20 º, parallel imaging factor 2, NEX 1).
Thanks a lot in advance, Ahmed
Hi Bruce, We are using a GE Signa 1.5 Tesla whole body system with an eight channel receive coil. Thanks for reply, Ahmed
Lainaus Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Ahmed,
The TR is quite short and the TE is probably too long. Ideally we use mprage if we can, but if it's SPGR we try to minimize the TE (ideally 2ms or less) and use a TR of around 20ms, and a somewhat bigger flip angle, maybe 30deg. What coil are you using and what field strength?
cheers Bruce
On Wed, 30 Jun 2010, Ahmed Abou Elseoud wrote:
Hello, We are starting to use FreeSurfer v4.5.0 for segmentation purposes and after running freesurfer and correcting the wm surfaces following the online instructions we still get abnormal surfaces (wm looks better after corrections, but gray matter still the same). We are suspecting the problem to be due to intensity problem in the original T1-weighted volumes and thus we would like to consult with you the T1 sequence we use to know if there is what we could fix/change about that.
T1-weighted scans were imaged using 3D FSPGR BRAVO sequence (TR 12.1ms, TE 5.2 ms, slice thickness 1.0 mm, FOV 24.0 cm, matrix 256 x 256, and flip angle 20 º, parallel imaging factor 2, NEX 1).
Thanks a lot in advance, Ahmed
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Hi Ahmed,
hmmm, with 2x acceleration are you getting a second scan? Not sure how good the SNR is. The 8 channels also sometimes can have poor signal at the vertex of the brain depending on coil geometry.
cheers Bruce
On Wed, 30 Jun 2010, Ahmed Abou Elseoud wrote:
Hi Bruce, We are using a GE Signa 1.5 Tesla whole body system with an eight channel receive coil. Thanks for reply, Ahmed
Lainaus Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Ahmed,
The TR is quite short and the TE is probably too long. Ideally we use mprage if we can, but if it's SPGR we try to minimize the TE (ideally 2ms or less) and use a TR of around 20ms, and a somewhat bigger flip angle, maybe 30deg. What coil are you using and what field strength?
cheers Bruce
On Wed, 30 Jun 2010, Ahmed Abou Elseoud wrote:
Hello, We are starting to use FreeSurfer v4.5.0 for segmentation purposes and after running freesurfer and correcting the wm surfaces following the online instructions we still get abnormal surfaces (wm looks better after corrections, but gray matter still the same). We are suspecting the problem to be due to intensity problem in the original T1-weighted volumes and thus we would like to consult with you the T1 sequence we use to know if there is what we could fix/change about that.
T1-weighted scans were imaged using 3D FSPGR BRAVO sequence (TR 12.1ms, TE 5.2 ms, slice thickness 1.0 mm, FOV 24.0 cm, matrix 256 x 256, and flip angle 20 º, parallel imaging factor 2, NEX 1).
Thanks a lot in advance, Ahmed
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
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Ahmed Abou Elseoud -
Bruce Fischl