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Dear Freesurfers,
In our centre we acquire T1 MPRAGE scans and phase-sensitive inversion recovery (PSIR) scans. Because of its better contrast between brain and non-brain I thought that we could use this scan in the freesurfer pipeline (v6.0) to refine the pial surface. I've already tried to use the -FLAIRpial flag (even though it's obviously not a FLAIR) but that actually makes it worse. Does anyone know if it is at all possible or have any experience with using PSIR scans in freesurfer and can point me in the right direction?
Thanks,
Best wishes
Chris
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Dr. C. Vriend | Assistant Professor Anatomy & Neurosciences - section Neuropsychiatry | Psychiatry Location VUmc | O|2 13W09 | De Boelelaan 1118, 1081 HZ Amsterdam T: + 31 (0) 6 25 69 49 12 | E: c.vriend@vumc.nlmailto:c.vriend@vumc.nl P: p/a sec. Anatomy & Neurosciences, postbus 7057, 1007 MB Amsterdam www.amsterdamumc.nlhttp://www.amsterdamumc.nl | www.vumc.nlhttp://www.vumc.nl/ | http://www.neuroscience-amsterdam.nl/?page_id=189 _____________________________________________________ VUmc disclaimer: www.vumc.nl/disclaimerhttp://www.vumc.nl/disclaimer
