Hi Bruce and Freesurfer Experts, I tried the suggestions below in these images but without complete resolution of the problem - there is an improvement but there is still stuff missing right at the front (last 3 to 4 slices). Is there anything else I can try in order to salvage these images ? As mentioned previously there is data there if I alter windowing parameters ...
Would be grateful for any help offered, Thanks. Mahinda On Tue, Jan 24, 2012 at 12:04 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > hmmm, could also be a low sensitivity region if the region around the eyes > doesn't have coil coverage. I would try putting a line of control points in > the white matter going from anterior and moving posteriorly until the > drop-off is not that big (i.e. until the T1.mgz has voxels==110 in the > white matter) > > > On Tue, 24 Jan 2012, Mahinda Yogarajah wrote: > > Hi, >> >> No problem - thanks for coming back to me. >> >> Imaging was carried out with a GE Excite II 3-T scanner using an eight- >> channel phased array coil. We acquired coronal 3D-T1 weighted fast spoiled >> gradient echo (FSPGR) (0.94 × 0.94 × 1.1 mm) which is what I am plugging >> into Freesurfer. >> >> There is actual data present - changing the windowing settings (brightness >> and contrast) at the front it is possible to make out both grey and white >> matter. It is at a low intensity compared with the rest of the brain. >> The >> data was acquired some time ago, and I am not sure what the source of drop >> off is. Thanks for your advice in advance. >> >> Thanks. >> >> M >> >> >> >> On Mon, Jan 23, 2012 at 11:07 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Mahinda, >> >> sorry, I meant to respond to this. It's hard to tell from the >> image - is there actually data in the frontal regions? What is >> the source of the drop-off? Is it a slab selective acquisition >> and is anterior/posterior the slab direction? >> >> cheers >> Bruce >> >> >> On Mon, 23 Jan 2012, Mahinda Yogarajah wrote: >> >> Dear Experts, >> >> Sorry if this is a repost, but I was not sure it got >> posted. >> >> I have a few subjects that I want to salvage and use >> where there appears to >> be significant signal inhomogeniety in the last few >> frontal slices (see >> T1.mgz in attached figure 1). Despite the use of >> control points (placed >> with careful adjustments of windowing parameters), I >> still can't encompass >> all of the the gyri right at the front (see >> brainmask.mgz coronal slice in >> figure 2). I would really appreciate some advice on >> how to proceed from >> here. Is placing white matter voxels in wm.mgz a >> possible solution ? Or is >> there another solution ? >> >> Thanks. >> >> M >> >> >> >> 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<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. >> >> >> >>
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