Hi Bruce,

Thanks for your reply.

The ?h.orig surfaces look accurate relative to the ?h.orig.nofix surfaces. If it helps, the ?h.smoothwm surfaces are intermediate between the ?h.orig and the ?h.white.

The intensity of the background ranges from 80-100, almost always in the lower half of that.

I reran the subject overnight, and you can see the result of that below, with the following layers/surfaces:

brainmask (bg)

wm (heat layer)

?h.orig.nofix (yellow)

?h.orig (green)

?h.smoothwm (blue)

?h.white (red)

Before rerunning it, I did not add any voxels back into the wm, but did clean up a few voxels and added some control points in distant areas. It seems like the surfaces changed a bit (and the wm.mgz file), and look a bit better overall, but some errors still remain in approximately the same places. More specifically, the main error on this slice is much better, but the voxels that were added in from the previous run on the small gyrus next to it have contributed to a different error.

Rerun version

Previous version (for comparison)

Thanks again, and let me know if any other info would be helpful.

Andy

On Mon, Jul 14, 2014 at 9:37 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Andrew

What does the ?h.orig look like? And what is the intensity volume in the background?

Cheers
Bruce

On Jul 14, 2014, at 4:18 PM, Andrew Schoen <schoen.andrewj@gmail.com> wrote:

Hi All,

I am currently running freesurfer on a group of subjects, some of which have some bright areas of GM near the surface of the pial line that is getting included as WM. As per the wiki article here I erased the offending GM from the wm.mgz file, and reran with the command:

recon-all -autorecon2-wm -autorecon3 -subjid SUBID

However, despite making the edits and rerunning, the ?h.white surfaces did not seem to adjust to the revised wm.mgz file (in fact, they looked pretty much the same as before). I found an exchange on the listerv here, where it was suggested that Max look at the ?h.orig.nofix files, to see if the changes were recorded there. I opened the ?h.orig.nofix (yellow) up next to the ?h.white file (red), and you can see those in the attached image wmedits.png. An image with the edited wm.mgz file as a heat overlay is included (wmeditswithwm.png)

I could see that the edits made to wm.mgz are being saved/read/interpreted correctly, and the nofix file was being saved correctly, but it doesn't seem to be influencing the surface file correctly.

Do you have any idea what might be going on here?

Thanks very much for any help you can provide,

Andrew

<wmedits.png>
<wmeditswithwm.png>
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