Hi Emma,

Thanks for your quick reply. I was no longer at the office when I saw your email. Please find attached the recon.all log file.

Best Mateus

2017-08-11 11:18 GMT-03:00 Boyd, Emma EBOYD2@mgh.harvard.edu:

Hi Mateus,

Please attach the recon-all.log file for your subject and I will take a look.

Best,

Emma

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of MATEUS ROZALEM ARANHA mateus.aranha@hc.fm.usp.br *Sent:* Friday, August 11, 2017 9:56 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Skullstriping problems

Hi,

I had problems with skullstriping. I ran recon-all and part of the skull is being considered as cortex in the segmentation. I tried to fix this using:

*recon-all -skullstrip -wsthresh 50 -clean-bm -subjid <subject name>*

and than

*recon-all -autorecon-pial -subjid <subject name>*

But nothing changed.

Do I need to run recon-all all over?

Thanks, Mateus

---

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Hi Mateus,

Could you clarify your original post for me:

By "nothing changed," do you mean that the brainmask.mgz is the same as before even though you used the new watershed threshold? Or that this changed but nothing downstream (like the aseg.mgz) changed?

Thanks, Emma

________________________________ From: MATEUS ROZALEM ARANHA mateus.aranha@hc.fm.usp.br Sent: Thursday, August 17, 2017 6:18:28 AM To: Freesurfer support list; Boyd, Emma Subject: Re: [Freesurfer] Skullstriping problems

Hi Emma,

Could you take a look at the recon-all.log file I sent you?

Best Mateus

Enviado do meu iPhone

Em 11 de ago de 2017, às 11:18, Boyd, Emma <EBOYD2@mgh.harvard.edumailto:EBOYD2@mgh.harvard.edu> escreveu:

Hi Mateus,

Please attach the recon-all.log file for your subject and I will take a look.

Best,

Emma

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of MATEUS ROZALEM ARANHA <mateus.aranha@hc.fm.usp.brmailto:mateus.aranha@hc.fm.usp.br> Sent: Friday, August 11, 2017 9:56 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Skullstriping problems

Hi,

I had problems with skullstriping. I ran recon-all and part of the skull is being considered as cortex in the segmentation. I tried to fix this using:

recon-all -skullstrip -wsthresh 50 -clean-bm -subjid <subject name>

and than

recon-all -autorecon-pial -subjid <subject name>

But nothing changed.

Do I need to run recon-all all over?

Thanks, Mateus _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.