Martin,

this is longitudinal processing, would you recommend a more aggressive or less aggressive skull strip?

Bruce,

I've not seen this issue on more than a handful of subjects. They're ALS, but I dont think that is the cause behind this. I'm unfamiliar with bias fields, but it's more likely than pathology. 

As for control points, there are no more than 5-7 voxels in that area over the span of 30 slices. Should I simply add to those? 

On Jun 28, 2013, at 11:19 AM, Martin Reuter wrote:

Hi Jonathan,

is this in cross sectional processing or in longitudinal?

One thing I notice is significant motion artifacts (ringing), which seem to lead to underestimation of WM, also you could fine tune the skull strip.

Best, Martin

On Jun 28, 2013, at 10:19 AM, Jonathan Holt <whatsdac@umich.edu> wrote:

Hi all,

I'm having a bit of trouble with one particular subject for which we brains for 4-5 different time points. The pial surface is consistently misplaced in the same area, see attached main/aux volume images. I'm hesitant to manually replace the white matter myself as I fear it wouldn't be as accurate. Suggestions on other methods to fix this?

The problem is always in the LH temporal right around the lateral inferior ventricle and the fusiform and other subcortical structures. 

<Screen Shot 2013-06-28 at 10.18.59 AM.png><Screen Shot 2013-06-28 at 10.14.50 AM.png>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---------------------------------

Dr. Martin Reuter

Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 

   mreuter@nmr.mgh.harvard.edu

   reuter@mit.edu

Web  : http://reuter.mit.edu 

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 . 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.