Hi Falk

Thanks so much for your reply.

I checked the brainmask.mgz file and I guess it looks ok. I copied the screenshot below:

I appreciate if you have any comment on that.

Thanks a lot

Mona

[cid:17ab68b4-1c80-4094-b54b-b550ea25c630]

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

________________________________ From: falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de Sent: Wednesday, August 21, 2019 5:42:54 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Nasiriavanaki, Zahra ZNASIRIAVANAKI@mgh.harvard.edu Subject: AW: [Freesurfer] recon_all hires

External Email - Use Caution

Hi Mona,

Potentially you have a bad skull strip resulting in a huge defect which will take a long time to correct. Simply fix your skull strip and you should be fine.

Best,

Falk

Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Nasiriavanaki, Zahra Gesendet: Dienstag, 20. August 2019 16:19 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon_all hires

Dear Freesurfer experts

I am doing recon-all on one of my subjects and it seems that it's stuck for days and not going through. I even re-run it and it's still stuck at the same spot as before.

I attached the log file and here is my command:

recon-all -all -s $subj -i /$subj/anat/$run/mT1v2.nii -expert expertopts/expert.opts -hires -mail zn025 -parallel

I appreciate any help.

Thanks

Mona

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

Hi Mona if you upload your gzipped and tarred subject dir we will take a look (or if it is somewhere accessible just point us to the network location and give us access)

cheers Bruce

On Fri, 23 Aug 2019, falk.luesebrink@med.ovgu.de wrote:

External Email - Use Caution

Hi Mona,

the brainmask looks quite good indeed. Have you had a look at the inflated surfaces with an overlay of the defect_labels? Then you can identify where the large error originates from and potentially can be fixed following the advices here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData and herehttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_free view, respectively.

What’s the resolution of your dataset? With very high resolution data (> 0.5 mm) even smaller defects will consists of many vertices which will take a long time to correct.

Best,

Falk

Von: Nasiriavanaki, Zahra ZNASIRIAVANAKI@mgh.harvard.edu Gesendet: Mittwoch, 21. August 2019 16:36 An: Lüsebrink, Falk falk.luesebrink@med.ovgu.de; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon_all hires

Hi Falk

Thanks so much for your reply.

I checked the brainmask.mgz file and I guess it looks ok. I copied the screenshot below:

I appreciate if you have any comment on that.

Thanks a lot

Mona

[IMAGE]

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

---

From: falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de Sent: Wednesday, August 21, 2019 5:42:54 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Nasiriavanaki, Zahra ZNASIRIAVANAKI@mgh.harvard.edu Subject: AW: [Freesurfer] recon_all hires

External Email - Use Caution

Hi Mona,

Potentially you have a bad skull strip resulting in a huge defect which will take a long time to correct. Simply fix your skull strip and you should be fine.

Best,

Falk

Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Nasiriavanaki, Zahra Gesendet: Dienstag, 20. August 2019 16:19 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon_all hires

Dear Freesurfer experts

I am doing recon-all on one of my subjects and it seems that it's stuck for days and not going through. I even re-run it and it's still stuck at the same spot as before.

I attached the log file and here is my command:

recon-all -all -s $subj -i /$subj/anat/$run/mT1v2.nii -expert expertopts/expert.opts -hires -mail zn025 -parallel

I appreciate any help.

Thanks

Mona

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129