Okay, so it didn't complete without error. I've attached the recon-all.log. Also, I was using another post op patient's MRI scans.

thanks so much, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing

Hi Mia

we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:

Hi Freesurfers,

I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where to run this and I don't see a page on the freesurfer site.

Thanks so much, m ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing

Hi Mia

this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)

cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:

Okay, so it didn't complete without error. I've attached the recon-all.log. Also, I was using another post op patient's MRI scans.

thanks so much, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing

Hi Mia

we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:

...

Hi Freesurfers,

I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Cool, it's running. Hopefully I did that right. Thanks for your help! ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, January 18, 2013 11:28 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing

it's run as part of recon-all. If you grab a new one and run

recon-all -make all ...

you should be all set Bruce

On Fri, 18 Jan 2013, Borzello, Mia wrote:

great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where to run this and I don't see a page on the freesurfer site.

Thanks so much, m ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 1:30 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing

Hi Mia

this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated)

cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:

...

Okay, so it didn't complete without error. I've attached the recon-all.log. Also, I was using another post op patient's MRI scans.

thanks so much, m ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing

Hi Mia

we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote:

...

Hi Freesurfers,

I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer