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.org
This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not
the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address
above, delete this email from your computer, and destroy any copies in any form immediately.
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:
External Email - Use Caution
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.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: 718-430-4011FAX: 718-430-3399
Email: mark.wagshul@einsteinmed.org
This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.
_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1FmyFbwTRNmR52lSeebeXqP5AQrT8BICIeBvN4vLgUbyu2lpM9gyRBF5Ovqeo_qLOcNE2LGLyAJP8LOx9XU7i517xPCEWkBClm2AuPJVUdMJ5hVXXKN5NYIoSAgb4E3VEtYbkmECZNi-O7Guk1WFmS9hELFojyd6s-fho0BkPGuEQd3zr2LxuSgJww3YRjaISg5s1v123K-TMaFDP1JiG1jc4_mj3S0CHJaQE0UYJ6wioN5jQHl2f1ndyzkbshFrwfXnQs9sjwYCzFddFUKnt7g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer