Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

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

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Loeffler, Martin martin.loeffler@zi-mannheim.de Sent: Tuesday, December 12, 2017 11:57:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

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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