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.mahinda@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 <fischl@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 <fischl@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



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