From fischl@nmr.mgh.harvard.edu Mon Apr  7 20:42:08 2008
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Re: problematic pial
Date: Mon, 07 Apr 2008 20:42:07 -0400
Message-ID: <Pine.LNX.4.62.0804072039000.25981@gate.nmr.mgh.harvard.edu>
In-Reply-To: <4b12b7b60804071112r538f40a8n5dff08d90e0b76ed@mail.gmail.com>
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Hi Jamie,

it's impossible to judge surface accuracy from one slice. You need to move=20
forwards and back a couple of slices to see if the surface is curving=20
sharply out of plane.

Can you explain a bit more about what is unique about this volume?  I=20
didn't really understand from your email. Is it a single subject MRI? Or=20
the average of some volumes processed using some nonlinear registration?

Bruce
  On=20
Mon, 7 Apr 2008, Jamie Hanson wrote:

> i think my attachment didn't make it through, the first time round.
> example pics now attached.
>
> thanks much,
> jamie.
>
>
>
>
> On Mon, Apr 7, 2008 at 1:10 PM, Jamie Hanson <jlhanson5(a)wisc.edu> wrote:
>> Hi Freesurfers-
>>
>>  I was trying to run freesurfer on a study template and was having
>>  major problems with pial surface generation. Orig and Main surfaces
>>  seem to be ok, but there are major missing chinks in pial surface.
>>  Just to give some background, the template was being using for
>>  Diffeomorphic Image Registration, so it is a very unique volume.I know
>>  it is likely it is an intensity value issue.I wondered what folks have
>>  done previously to correct similar issues?
>>
>>  It appears to be across a massive proportion of the brain, so
>>  correcting by hand (by altering intensity values seems a bit labor
>>  intensive and perhaps questionable in terms of reliability). I also
>>  thought of trying to rerun some of the initial preprocessing
>>  (autorecon1 + 2) with some more 'expert settings'. Initially, I was
>>  running with no skull strip and no n3 flag (b/c the template has
>>  already been skull-stripped and massive preprocessed), but was looking
>>  for some additional advice and guidance.
>>
>>  Any thoughts or suggestions would be greatly appreciated.
>>
>>  Best,
>>  jamie.
>>
>>
>>
>>
>>  --
>>  Jamie L. Hanson
>>  Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research =
Lab
>>  University of Wisconsin - Madison
>>  1500 Highland Avenue
>>  Madison, WI 53706
>>  ***Please note my new email: jamielarshanson(a)gmail.com***
>>
>
>
>
>

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