Hi Bruce,
I edited the wm.mgz with the recon-editing tool this time, removing the problem areas near this defect (primarily lots of dura originally included), and confirmed that my edits remained after re-processing.  However, the left STG is still being removed, images attached (red is the lh.orig.nofix with lh.defect_labels overlayed, yellow is lh.white).  The entire left STG is still being marked as a defect despite my edits.  Any suggestions?

Thanks,
Matt
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [MHIBERT@mgh.harvard.edu]
Sent: Tuesday, June 06, 2017 5:22 PM

To: Freesurfer support list
Subject: Re: [Freesurfer] 7T recon

Ah ok, thanks Bruce.

Matt
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu]
Sent: Tuesday, June 06, 2017 4:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] 7T recon

Hi Matt
we keep track of edits by setting erased voxels to 1, not 0. If you do
the editing within freeview using the "recon edit" tool, this will happen
automatically

cheers
Bruce
On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote:

> Hi Bruce,
> Thanks again for your help so far.  I've tried removing the problem voxels from the wm.mgz (setting their value to 0), saving the wm.mgz, and then running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT -xopts-use -openmp 2".  However, the edits to the wm.mgz are not incorporated and the surfaces are not changed; when I open the wm.mgz again, the voxels I removed are now present again.  What am I doing wrong?
>
> Thanks,
> Matt
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu]
> Sent: Friday, May 26, 2017 1:57 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] 7T recon
>
> yes, and autorecon3
> On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
>
>> Thanks Bruce.  After I remove the problem voxels in wm.mgz, do I then re-run the recon from autorecon2-wm?
>>
>> Thanks,
>> Matt
>> ________________________________________
>> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu]
>> Sent: Friday, May 26, 2017 1:40 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] 7T recon
>>
>> Hi Matt
>>
>> yes, that means there was a topological defect that was incorrectly
>> fixed. If you load the wm.mgz over the lh.orig.nofix, then in the
>> orig.nofix load the file defect_labels as an overlay and change the overlay
>> settings to that the min is 1 and click the "use overlay color" button it
>> will show you the regions of the surface that are defective. You will then
>> need to edit the wm.mgz to remove the handle/hole that is the defect.
>>
>> cheers
>> Bruce
>>
>>
>> On Fri, 26 May 2017, Hibert, Matthew Louis wrote:
>>
>>> Hi All,
>>> I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T
>>> and while most look good, 4 of the subjects have a similar section of the
>>> left STG removed from the final surfaces (picture attached).  In all 4
>>> subjects the entire left STG is included in the wm.mgz and lh.orig.nofix
>>> (red), but a portion has been removed in lh.orig (yellow), so the problem
>>> seems to occur in the -fix stage of autorecon2.
>>>
>>> How can I go about correcting this issue?
>>>
>>> Thanks,
>>> Matt
>>>
>>>
>>
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>>
>>
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