Hi Martin,

We've taken a look at the scans you uploaded, and unfortunately it won't be possible to run the standard recon-all on your subject. Recon-all is not designed to work on scans with such large lesions. If you are interested, there may be a way to generate a reasonable model of the right hemisphere.

Best,

Bram

Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin

-----Ursprüngliche Nachricht-----
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the running recon-all process, and set control points and run again? Investing some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> ________________________________________
> Von: freesurfer-bounces@nmr.mgh.harvard.edu
> [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von
> "Bruce Fischl [fischl@nmr.mgh.harvard.edu]
> Gesendet: Montag, 11. Dezember 2017 22:47
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
>
> Hi Martin
>
> a defect that large means that something big went wrong (skull or dura
> attached, etc...). Try looking at the ?h.orig.nofix and/or the
> ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find
> defect 9
>
> cheers
> Bruce
>
>
> On Mon, 11 Dec 2017, Loeffler, Martin wrote:
>
>>
>> Dear FreeSurfer team,
>>
>>
>>
>> For a case report I'm running recon-all on a patient with a giant
>> arachnoid cyst in the left hemisphere. It gets stuck at this point (last message):
>>
>> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
>>
>> XL defect detected...
>>
>> It is stuck here since a whole day now, so I'm not expecting it to
>> advance.
>>
>> Following this post:
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I looked at the wm.mgz, but did not find huge errors.
>>
>> Do you have any ideas what the problem might be or what I can do to work around it?
>>
>>
>>
>> Thanks,
>>
>> Martin
>>
>>
>>
>>
>>
>>
>>

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