Dear Freesurfer Experts, Would it be easier to upload a typical example of the data I am trying to salvage, in order to get some hints on how I might proceed with this problem of loss of frontal signal drop off ?
Thanks in advance. Mahinda On Thu, Feb 23, 2012 at 2:06 AM, Mahinda Yogarajah <y.mahi...@gmail.com>wrote: > 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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