when you bring it up in freeview does it properly show left and right? If
it ever went through analyze as a format you will have lost the
information that lets us distinguish left from right

cheers
Bruce
On Fri, 14 Dec 2018,
Geha, Paul wrote:

> It is NIFTI format.  
> ——————————————————
> 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
>
>
>
>       On Dec 14, 2018, at 10:53 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>
> 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 (https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu.ox.ac.uk%2Fcrystal%2Fla
> bel.cgi%3Fid%3D110&amp;data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8c
> bebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317&amp;sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnMN
>       MMSLiAGyXq734%3D&amp;reserved=0<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu.ox.ac.uk%2Fcrystal%2Fl
> abel.cgi%3Fid%3D110&amp;data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8
> cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317&amp;sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnM
>       NMMSLiAGyXq734%3D&amp;reserved=0>). 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
>
>
>
>             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:
>
>                          External Email - Use Caution
>                   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
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