External Email - Use Caution

Dear FreeSurfer experts,

I have both T2 and FLAIR images for the majority of the subjects in my study, and I want to use them to improve pial surface reconstruction during recon-all as explained in [1].

My questions are:

1) In general, should I prefer FLAIR over T2, or the other way around? 2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for others, in the same study? We will perform manual QC after the recon-all run and exclude bad quality images, so I feel it should be fine, but I wanted to hear your opinion.

Best,

Tim

[1] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimpr...

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany