Hi Chris

not directly. You will want to use the mprage for generating the surfaces as we don't expect fluid to be bright

cheers Bruce On Sat, 5 Jan 2019, Vriend, C. (Chris) wrote:

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Hi Bruce,

So sorry, your reply totally escaped my attention!

Attached a screenshot of a PSIR scan. Do you think that Freesurfer can work with these contrasts?

Thanks,

Chris

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Van: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Namens Vriend, Chris Verzonden: donderdag 16 augustus 2018 8:12 Aan: 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu Onderwerp: [Freesurfer] PSIR to refine pial surface?

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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.nl P: p/a sec. Anatomy & Neurosciences, postbus 7057, 1007 MB Amsterdam www.amsterdamumc.nl  |  www.vumc.nl | http://www.neuroscience-amsterdam.nl/?page_id=189

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