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
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 mailto: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:
* 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 <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.wagshul@einsteinmed.org <mailto:mark.wagshul@einsteinmed.org>_ einstein-logo-rgb 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 list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1FmyFbwTRNmR52lSeebeXqP5AQrT8BICIeBvN4vLgUbyu2lpM9gyRBF5Ovqeo_qLOcNE2LGLyAJP8LOx9XU7i517xPCEWkBClm2AuPJVUdMJ5hVXXKN5NYIoSAgb4E3VEtYbkmECZNi-O7Guk1WFmS9hELFojyd6s-fho0BkPGuEQd3zr2LxuSgJww3YRjaISg5s1v123K-TMaFDP1JiG1jc4_mj3S0CHJaQE0UYJ6wioN5jQHl2f1ndyzkbshFrwfXnQs9sjwYCzFddFUKnt7g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1tspEfj7-Hpjd3VybY_f2pHHXH4Uhmqbfq4U2szlQ89XMdf7Dq59VccLpil3h6qr1JrdVTRT_pIAy4og_twvbu5XcW3zBTqhFX0yEfpZweGAUi-KM9QhrDEvQ_xJn49Zs441yUQaMcF1WR9JGtmUBeR0QKXnRmkA2L7tUr1Eyj7TrQFYA_29-57SIaV3K99NKVN0qJVYevUyWX12-s6P5S-uUPJekwqF9aA9gRynMyYRn55vZ-AS_0-oD9h3chEq4E-JdkcdRHMU3Ns_imLWT5w/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1FmyFbwTRNmR52lSeebeXqP5AQrT8BICIeBvN4vLgUbyu2lpM9gyRBF5Ovqeo_qLOcNE2LGLyAJP8LOx9XU7i517xPCEWkBClm2AuPJVUdMJ5hVXXKN5NYIoSAgb4E3VEtYbkmECZNi-O7Guk1WFmS9hELFojyd6s-fho0BkPGuEQd3zr2LxuSgJww3YRjaISg5s1v123K-TMaFDP1JiG1jc4_mj3S0CHJaQE0UYJ6wioN5jQHl2f1ndyzkbshFrwfXnQs9sjwYCzFddFUKnt7g%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D04%257C01%257CMark.wagshul%2540einsteinmed.org%257C6bb22b2e969446c2f20e08d9215c9cbc%257C9c01f0fd65e040c089a82dfd51e62025%257C0%257C0%257C637577503918609620%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DvdFzL2nl1GOSCcHMWcxmgbltlXp1ZqeGLNMcnzMiRHk%253D%26reserved%3D0>
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