External Email - Use Caution
Thanks. I've never used this command before to register the FLAIR, but I'm getting the following error:
[mwagshul@loginnode2 mri]$ tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta --targ orig.mgz cd /gs/gsfs0/users/mrrc-all/PROJECTS/HOLTZER/MSAGING/MS_PROCESSING/2019-10049-044/mri freeview -transform-volume -viewport cor -v orig.mgz:visible=1:name=orig.mgz(targ) /gs/gsfs0/users/mrrc-all/PROJECTS/HOLTZER/MSAGING/MS_PROCESSING/2019-10049-044/mri/orig/FLAIRraw.mgz:name=FLAIRraw.mgz(mov):reg=/gs/gsfs0/users/mrrc-all/PROJECTS/HOLTZER/MSAGING/MS_PROCESSING/2019-10049-044/mri/transforms/FLAIRraw.lta /public/apps/freesurfer/7.1.0/bin/fsvglrun: line 20: conditional binary operator expected /public/apps/freesurfer/7.1.0/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /public/apps/freesurfer/7.1.0/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then' [mwagshul@loginnode2 mri]$
Thanks for any advice on the issue here.
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
[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.
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.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
[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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1FmyFbwTRNmR52lSeebeXqP5AQrT8BICIeBvN4vLgUbyu2l...https://secure-web.cisco.com/1uodFcWge5D7CiXVGF76MUxbUdhgVkjEXRSm2A6hHtdB8SeclT8I1DnipEjD5N5xkDVmpFdX4aRkpwTIEB5KehFnabUNb0d0_Bo2qhEm8v88f_5ODScYkfwmKTW4UHJyt7ZCaUXX6KxURh7cOZjIv4IQyjXRizb6oYI9rtMui3fIH67OVzRrIWVQHGdUOUg_3Po_2l2xJcXHCIktrFNQ08W7rr-NiYOKl7BD9U4LCLXUiLsj3-Ny1FVazZZzZF8odUcBTpAVoBzuNX-o2iMj92Q/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
