External Email - Use Caution 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! 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.wags...@einsteinmed.org<mailto:mark.wags...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Tuesday, June 1, 2021 6:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all errors 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: 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.wags...@einsteinmed.org<mailto:mark.wags...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Thursday, May 27, 2021 6:13 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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.wags...@einsteinmed.org<mailto:mark.wags...@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. 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