Re: [Freesurfer] Frontal signal drop out

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.eduwrote:

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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