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.

 

 

 

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

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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

 

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