Hi Devika
these types of huge defects usually mean something dramatic has gone
wrong with e.g. the skull stripping. Even if it completes it is unlikely
to generate accurate surfaces. Check the ?h.inflated.nofix and
?h.orig.nofix over the wm.mgz and you will likely find the issue quicky
cheers
: Friday, January 31, 2020 5:38 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] XL defect in recon-all
External Email - Use Caution
Hi,
I am running recon-all on Freesurfer version 6. Few of my subject's have XL
defect error as shown below.
CORRECTING DEFECT 0 (vertices=
External Email - Use Caution
Hi,
I am running recon-all on Freesurfer version 6. Few of my subject's
have XL defect error as shown below.
CORRECTING DEFECT 0 (vertices=18408, convex hull=3300, v0=0)
XL defect detected...
This has been running for more than a day.
How can I fix
oun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, May 23, 2019 3:46:30 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] XL defe
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] XL defect in recon-all
You can look at this tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
But if you are using high res, I would run high res stream I put
together for the HCP:
ftp://surfer.nmr.mgh.harvard.edu/pub
You can look at this tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
But if you are using high res, I would run high res stream I put
together for the HCP:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/
On 5/23/19 2:59 PM, Barletta,
Dear Freesurfers,
I tried to launch "recon-all -all" for an high-resolution 7T 0.75 isotropic
MEMPRAGE, but the process got stuck on a XL defect in rh, numbered 54,
measuring over 20,000 voxels!!
How do I check, and eventually fix, this defect?
Thank you,
Vale
_
