Doug,

 

Thanks. The one thing I thought of – the FLAIR data were hi-res 3D FLAIR which have a pretty long T2 and not great grey/white contrast (it’s an MS project, so mostly acquired for quantifying lesion load). Not sure if this would affect the calculations. I tried playing around with the T2_min/max_inside/outside parameter going into mris_place_surface, but that didn’t seem to help.

One more thing. I don’t see this in the recon-all.log file, but when I try to individually run mris_place_surface, it quits with a segmentation fault. Not sure if that helps, or why this error wouldn’t show up in the log file.

 

Thanks for the help!

 

 

 

OK, I'll have to take a look at the data. Someone will be in touch about getting it.

        External Email - Use Caution        

        External Email - Use Caution        

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: 718-430-4011

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.

 

 

_______________________________________________

Freesurfer mailing list

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

 

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://secure-web.cisco.com/1ucxeQYS68-2vGG3TlU2NsAjIdtUpFT30cVUdCcfUHG3Mdvf7_4Lzvg9eNvE0ydHVtdDzd1NjAvJS2Y49YFyViFmweOH4R8sjIX9T_xVdw6yCruNa_3YUSLs5RDqSEBqLYQ6eat1gksfd2Q7cw-KIvXYdPxqGLQRoWVciBEc_sDwI81Q0KiVJB-c04Z1nHJsxhQZTabdafhQa6M-NerIrQu8iwRmXzhRo0bizUb7-VTtSRBpmcdYGn_oYUa1XaAsgznc5mORPVSSLLOz5RAUPFQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer