Re: [Freesurfer] anterior temporal lobe problems

[Khoa Nguyen]

Control points do a good job in fixing the problem for me. You just have 
to put a string of control points (not too many) on the white matter 
strips for every 2-3 slice.

-Khoa
On Thu, 3 Nov 2011, Louis Nicholas Vinke wrote:

Hi,
Some other potential explanations for poor surfaces in this area are 
addressed here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfacesnearthemedialwall.2Chippocampus.2Candamygdalaaren.27taccuratelyfollowingthestructuresthere.HowcanIfixthis.3F

"This region tends to be furthest away from the coils receiving the MR 
signal, potentially late to myelinate in individuals under 20 years old, very 
thin white matter in general, and is in close proximity to regions of 
susceptibility."

I'm not aware of any flags which could begin to fix the surfaces in those 
areas automatically.
-Louis

On Wed, 2 Nov 2011, Freesurfer Local Archive wrote:

 Michael,

 I had a similar problem with about 10% of pediatric datasets I used.
 In my case the problem also often included anterior and ventral
 surface of the frontal lobes. Much like you I looked at possible
 explanations and a medical physicist and a radiologist I worked with
 blamed inaccuracies entirely on chemical shift. Adding control points
 at least in temporal lobes generally provided only moderate
 improvements.

 Greetings,

 Jacek


 On Wed, Nov 2, 2011 at 4:02 PM, Michael Harms <mha...@conte.wustl.edu>
 wrote:
> 
>  Hi guys,
>  We have a sample of 150+ pediatric brains that we pumped through FS 5.1,
>  and in an easy majority of them the white/pial surface accuracy in the
>  anterior temporal lobe is poor.
> 
>  I know that this is an area where problems have frequently been
>  reported.  What is it about that area in particular that makes it
>  difficult to get accurate surfaces?  (Is the contrast and SNR in that
>  area inherently worse?)  And, short of a large time commitment of
>  control point and wm.mgz editing, are there any flags/tweaks that we
>  could attempt to fix the problem in a more automatic fashion?
> 
>  thanks,
>  -MH
> 
> 
>  --
>  Michael Harms, Ph.D.
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