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.luesebr...@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 <znasiriavan...@mgh.harvard.edu>
Gesendet: Mittwoch, 21. August 2019 16:36
An: Lüsebrink, Falk <falk.luesebr...@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.luesebr...@med.ovgu.de <falk.luesebr...@med.ovgu.de>
Sent: Wednesday, August 21, 2019 5:42:54 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Nasiriavanaki, Zahra <znasiriavan...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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