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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
____________________ 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.wagshul@einsteinmed.orgmailto:mark.wagshul@einsteinmed.org
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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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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External Email - Use Caution 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.larkspurmailto: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.wagshul@einsteinmed.orgmailto:mark.wagshul@einsteinmed.org
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