Hi Danielle
what does it look like withouth the FLAIR postprocessing? And what FLAIR sequence are you using? We have only ever used the T2-space FLAIR and have been told that it works great with that, but not as well with other FLAIR variants.
cheers Bruce
On Tue, 22 Apr 2014, Danielle Miller wrote:
Hi Freesurfer Experts,
I seem to be having some difficulty with reconing a healthy young adult. I have tried running this on multiple different computers and multiple different versions (5.3 and 5.1) and all return the same weird recon (see attached image). I have used the same sequence and commands on another subject and the recon returned fine.
This participant did not have excess motion and the orig.mgz file looks fine. Please let me know if there is any more information I could provide that would be of use.
Commands used:
5.3: recon-all -all -FLAIR (FLAIR image) -subjid (SUBJID) -FLAIRpial -hippo-subfields recon-all -all -subjid (SUBJID)
5.1: recon-all -all -subjid (SUBJID) -hippo-subfields recon-all -all -subjid (SUBJID)
Thanks, Danielle Miller -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118
VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130