Hi Charles,

the FLAIRpial is a recent addition and has only been added to the cross sectional stream so far. I can take a look at porting this to the longitudinal stream but probably not for 5.2.

Best, Martin

On Feb 7, 2013, at 7:23 AM, Charles Malpas c.malpas@student.unimelb.edu.au wrote:

Dear Freesurfer Ninjas,

I have been playing around with the new beta version, and am very interested in the -FLAIRpial option. I have been using this successfully on cross-sectional runs, but would like to extend it to cross sectional runs.

I have played around with trying to get this to work, including copying FLAIRconf.mgz to the longitudinal run directions (subjid.long.template) and the recon-alll -long command with -FLAIRpial. Although this runs, it produces cortical thickness estimates that appear underestimated on visual inspection.

Is there a better way to incorporate -FLAIRpial on longitudinal runs? Is it even possible at this stage?

Many thanks for your time,

• Charles

-- Charles Malpas Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010

Melbourne Brain Centre @ RMH Neuropsychiatry Research Group Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas@student.unimelb.edu.au Skype: charles.malpas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

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