what is your input data format? On Fri, 14 Dec 2018, Geha, Paul wrote:

Dear Bruce,

Thank you for your reply.

However, we are obtaining an odd result with FreeSurfer when we examine the volume of the left and right accumbens. In the UK BioBank data >20K subjects freesurfer segmentations the left accumbens is clearly significantly larger than the right accumbens ( http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=110 http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=110). Also, the attached paper used freesurfer and found left accumbens > right. In our hands, and in 2 different data sets collected in two different sites, we obtain the opposite with FreeSurfer (right accumbens > left accumbens).

Furthermore, when we segment these same data sets with FIRST from FSL we do obtain Left accumbens > right Accumbens in both data sets in agreement with the literature.

Any help in solving this discrepancy is much appreciated.

Regards, Paul —————————————————— Paul Geha, MD Assistant Professor of Psychiatry Yale School of Medicine Assistant Fellow, The John B. Pierce Laboratory Email: paul.geha@yale.edu Tel:(203)903-4334

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On Dec 13, 2018, at 3:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Meena

it shouldn't. We reorient everything to radiological

cheers Bruce On Thu, 13 Dec 2018, Meena M. Makary wrote:

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Hi; I am wondering if the orientation of the input data to recon-all (i.e. Neurological Vs. Radiological) produces different results in terms of laterality (right vs. left)? Thanks; --Meena — Meena M. Makary, Ph.D. Assistant Professor | Cairo University Postdoctoral Fellow | Yale University School of Medicine Postdoctoral Associate | The John B. Pierce Laboratory Postdoc Committee Chair | The John B. Pierce Laboratory Career Development and Mentoring Manager Elect | OHBM Student and Postdoc SIG 290 Congress Avenue, New Haven, CT 06519 +1 (475) 731-5592