I have a pretty terrible T1 from a child. The functional data, acquired first, are fine. But the T1, acquired last, has pretty serious movement artifact (attached image). While I would not use this particular scan for morpohological analysis, it seems like a reasonable surface reconstruction could be used to project functional data.
My problem is, the original T1 seems to have a better grey-white boundary than the intensity-normalized image. Is there a way to adjust the parameters for normalization to try to improve this? Would this be adjustments to only the autorecon1 series? That is, if I can improve the contrast, should autorecon2 and 3 run normally? Are control points the only way to improve this?
Anthony
Hi Anthony
yes, you can using the expert options to change the parameters of mri_normalize. Motion could mess it up, as it assumes a sharp enough gradient at the gray/white boundary to prevent the white matter region growing from crossing into the gray matter. Make sure that it's not just the window levels of the visualization though. Usually when the normalization fails you'll see regions of gray matter that have been set to 110, not just reduced contrast.
cheers Bruce
On Tue, 11 Sep 2012, Anthony Dick wrote:
I have a pretty terrible T1 from a child. The functional data, acquired first, are fine. But the T1, acquired last, has pretty serious movement artifact (attached image). While I would not use this particular scan for morpohological analysis, it seems like a reasonable surface reconstruction could be used to project functional data.
My problem is, the original T1 seems to have a better grey-white boundary than the intensity-normalized image. Is there a way to adjust the parameters for normalization to try to improve this? Would this be adjustments to only the autorecon1 series? That is, if I can improve the contrast, should autorecon2 and 3 run normally? Are control points the only way to improve this?
Anthony
Hi Bruce,
Do you mean use the flags for the individual mri_normalize command from the command line? If so, which parameters are best to modify in this situation?
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize
Anthony
On 9/11/12 3:06 PM, Bruce Fischl wrote:
Hi Anthony
yes, you can using the expert options to change the parameters of mri_normalize. Motion could mess it up, as it assumes a sharp enough gradient at the gray/white boundary to prevent the white matter region growing from crossing into the gray matter. Make sure that it's not just the window levels of the visualization though. Usually when the normalization fails you'll see regions of gray matter that have been set to 110, not just reduced contrast.
cheers Bruce
On Tue, 11 Sep 2012, Anthony Dick wrote:
I have a pretty terrible T1 from a child. The functional data, acquired first, are fine. But the T1, acquired last, has pretty serious movement artifact (attached image). While I would not use this particular scan for morpohological analysis, it seems like a reasonable surface reconstruction could be used to project functional data.
My problem is, the original T1 seems to have a better grey-white boundary than the intensity-normalized image. Is there a way to adjust the parameters for normalization to try to improve this? Would this be adjustments to only the autorecon1 series? That is, if I can improve the contrast, should autorecon2 and 3 run normally? Are control points the only way to improve this?
Anthony
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Hi Anthony
I would start out with the intensity above and below thresholds. Making them narrower will make the normalization less aggressive.
cheers Bruce On Wed, 12 Sep 2012, Anthony Dick wrote:
Hi Bruce,
Do you mean use the flags for the individual mri_normalize command from the command line? If so, which parameters are best to modify in this situation?
http://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize
Anthony
On 9/11/12 3:06 PM, Bruce Fischl wrote:
Hi Anthony
yes, you can using the expert options to change the parameters of mri_normalize. Motion could mess it up, as it assumes a sharp enough gradient at the gray/white boundary to prevent the white matter region growing from crossing into the gray matter. Make sure that it's not just the window levels of the visualization though. Usually when the normalization fails you'll see regions of gray matter that have been set to 110, not just reduced contrast.
cheers Bruce
On Tue, 11 Sep 2012, Anthony Dick wrote:
I have a pretty terrible T1 from a child. The functional data, acquired first, are fine. But the T1, acquired last, has pretty serious movement artifact (attached image). While I would not use this particular scan for morpohological analysis, it seems like a reasonable surface reconstruction could be used to project functional data.
My problem is, the original T1 seems to have a better grey-white boundary than the intensity-normalized image. Is there a way to adjust the parameters for normalization to try to improve this? Would this be adjustments to only the autorecon1 series? That is, if I can improve the contrast, should autorecon2 and 3 run normally? Are control points the only way to improve this?
Anthony
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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