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%2Flabel.cgi%3Fid%3D110&data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8c bebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317&sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnMN MMSLiAGyXq734%3D&reserved=0<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu... abel.cgi%3Fid%3D110&data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8 cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317&sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnM NMMSLiAGyXq734%3D&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 Career Development and Mentoring Manager Elect | OHBM Student and Postdoc SIG 290 Congress Avenue, New Haven, CT 06519 +1 (475) 731-5592