OK, I'll have to take a look at the data. Someone will be in touch about
getting it.
On 6/1/2021 11:02 AM, Mark Wagshul wrote:
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It works fine in 6.0, was in 7.1. The registration looks fine (the
FLAIR is brain extracted, while the orig.mgz is not, is this expected,
or was that my error, I don’t recall which FLAIR image I fed in).
Mark
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*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve
*Sent:* Thursday, May 27, 2021 6:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all errors
Can you check the registration of the FLAIR and T1?
cd subject/mri
tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta
--targ orig.mgz
On 5/20/2021 4:33 PM, Mark Wagshul wrote:
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Hi. I’m trying to run recon-all, with T1 and FLAIR images and
running into errors, which seem to be associated with the FLAIR
refinement of the pial surface.
recon-all -s 2019-10049-045-SP –FLAIR
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz
-FLAIRpial -all
1.Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2.cat /proc/version: Linux version
2.6.32-696.6.3.el6.694g0000.x86_64
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur
<mailto:root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur>) (gcc
version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul
12 02:19:57 UTC 2017
3.uname –a: Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1
SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
4.recon-all.log attached
Thanks!
Mark
____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
Email:_mark.wags...@einsteinmed.org
<mailto:mark.wags...@einsteinmed.org>_
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