Hi Bruce,

Thanks a lot for your help thus far. I've edited, computed, and applied the average bias to the error subjects' orig.mgz files. However, I'm not sure how to re-run all autorecon steps for these cases using the newly created orig.mgz (with bias applied). Thoughts?

Thanks,

Adam

Hi Adam

it depends on the source of the bias. If it is fixed in the coordinate 
system of the scanner you could correct a few, then try using 
mri_compute_bias and mri_apply_bias to see if it helps (it computes an 
average bias field in scanner coords, then applies it to a new dataset)

cheers
Bruce
On 
Wed, 23 Jul 2014, Adam Mezher wrote:

> 
> Hi Bruce,
> 
> Yeah that was my thinking as well. So, if after running 500 subjects through
>  FS and 100 need similar edits in the anterior temporal lobes, we will have 
> no choice but to perform manual edits for each case individually?
> 
> Thanks for clarifying!
> 
> Adam Mezher
> 
> >
> 
> >
> 
> Hi Adam
> 
> I don't think so as how would we don't know where the anterior temporal 
> lobe at that stage in the process.
> Bruce
> 
> 
> On 
> Tue, 22 Jul 2014, Adam Mezher wrote:
> 
> > Hi FreeSurfer group,
> > I was wondering if there is a way to include control points in my command
> > line when I run recon-all. We are working with a large dataset and many of
> > the subjects have underestimations in the anterior temporal lobes so it
> > would be beneficial to expand the WM surface slightly on numerous cases
> > rather than doing control point edits on each case individually.
> > 
> > Thank you,
> > Adam Mezher
> > 
> 
> 
>
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