External Email - Use Caution Dear Freesurfer is very sensitive to: 1-memory of system 2- coordinate system of FLAIR image 3- contrast equalization Check them I hope be usefull Nader
On Thu, 3 Jul 2025, 22:54 Mojdeh Zamyadi, <[email protected]> wrote: > External Email - Use Caution > > Hi FreeSurfer developers, > > I’m attempting to use FLAIR images to improve the segmentation quality of > some of my subjects after successfully running recon-all –all with the T1 > images. After QCing the initial results some segmentation needed > improvement which is why I am trying to use the FLAIR images on the > recon-all –all results with T1. > > > > This is the command I am using: > recon-all -s ${subject_id}_T1 -FLAIRpial -autorecon2 -autorecon3 > > but I am getting errors at the “mris_place_surface” stage. > > I have also tried manually running mri_normalize first and then running > recon-all with the –FLAIRpial flag (command below), but I still get the > same errors. > mri_normalize $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.mgz > $SUBJECTS_DIR/${subject_id}_T1/mri/FLAIR.norm.mgz > > > > I have attached my recon-all.log file here in case it’s of any use. > > > > Additional info: > 1- recon-all --version > > freesurfer-macOS-darwin_x86_64-8.0.0-20250205-0f2bd3a > > > > 2-Mac info: > ProductName: macOS > > ProductVersion: 15.5 > > BuildVersion: 24F74 > > > > 3- uname -a > > Darwin iMac.local 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:53:26 > PDT 2025; root:xnu-11417.121.6~2/RELEASE_X86_64 x86_64 > > > > Also, a note that we have been able to run recon-all v6 with –FLAIR flag > on the same subject on an older Mac system. > > > > I would appreciate any insights you might have to how to improve my > results using Flair images using v8 of FreeSurfer. > > > > Thanks, > > *Mojdeh Zamyadi, MSc (she/her)* > > Research Coordinator (Imaging) > > Centre for Youth Bipolar Disorder > > Centre for Addiction and Mental Health > > 80 Workman Way, Toronto > <https://secure-web.cisco.com/1Dz4UWKQ4rts8wI7Zz644R8rIsb-ohkBF1wZU1t03gMIGD0dhcGTezCVbwtvVE-B9tpzZme1kngeFQnUiun5sgbBj1lJn_655_-4vmQyq-DcylvXjRz8XAH55IL7iefLvQngdjMSnK01_nmuSdP5FztsXV5QZCO_aSsQty8yvCI2R82zPmpExcShC6vMqys-oJfZSFq8qCr3Nt-qvlV2JpUpp0KOGkVZJPXnJXgupDM68qgD5wO7DPnILw4ob_2wmSAR2iH91kVHxzJYbo-ByyqqC6n1KuQtKEDdOquHi_T2plLrb25ndNOnl7_YYqAle/https%3A%2F%2Fwww.google.com%2Fmaps%2Fsearch%2F80%2BWorkman%2BWay,+Toronto?entry=gmail&source=g> > > 416-535-8501 ext. 33278 > > > > Twitter: @CYBDatCAMH > <https://secure-web.cisco.com/1YOInhbSeEqszoMsC5o-oTzaa5eOkFEeEi14Qwx4Faci68LRdSVkmnVxCWh5U5Xp19yfHBSMCAV0Yg_R76-ft7YWgbA9OC9F1hMkM_OMu_BMBPUdcmQ9wlHYQS2WEhgu0H_G1vAs2t51crm0Gp5aUx5OdnDjAfBFshGpaQKx_IKXwxd9A1trPLUUAQKewCrMIW88MYLwAKuMjD3MfJdzMxb2pIVTuoGVFmghhymqDvau9itJmngDQMYnzPufjxKEy5wP5Qv5JAfDJ2gKIL-3rQXhGui0Y7RvQpvy6J6EPZZBk2JU-N6uEQU7kj7a40IZEuMwdeGGWtgiwW6pCzrVn5w/https%3A%2F%2Ftwitter.com%2FCYBDatCAMH> > > Website: camh.ca/CYBD > <https://secure-web.cisco.com/1-8ab9JMFlspDu1rE_5j9UF0W-Y4o0EXEfZACxBbGkZC9NrRp_Ny15ALwRReFbiSTRXxkGwS1TjyHA2mBNj49U1YItekrG4k3vhCmmagTUo63eFlSVogGhSASNUoedpoG6auMFMUR9OFxZKHMZ81_LmxydeSz206TXwv7VLSQTxF4MEuxYfFsXeQofbUb1Y1eMPPzWuTuhukGPUnASHZsIzzaHGSJl1QAToPmLXWz_IFIErySJOte0TrEn8z0YWKQay1O4ijkBrf0iqhJ_IxbvPFfdStueCPUC9xOxV91ct4TGzPsbbaCncXFbJqhNYjT0k9qpk3T48Ffx2GhU1iUpQ/https%3A%2F%2Ft.co%2FUXatZtSnyN> > > > > [image: cid:[email protected]] > > > > *If you are in crisis or need urgent help: * > > · Call the Kids Help Phone: 1-800-668-6868 or text 686868 > > · In Toronto, contact the Youthdale Crisis Service Line: > 416-363-9990 > > · Go to a local hospital emergency room > > · Call 911 > > > > > > > > > > > > > > > > > > > > CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is > for the sole use of the intended recipient(s) and may contain confidential > and privileged information. 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