External Email - Use Caution Thank you Bruce for your reply and the helpful information. Our data never went through Analyze format (we converted the data from dcm > NIFTI using mricron). FreeView reads the data appropriately (confirmed by attaching a Vitamin D pill to one of our subject's right side).
Thanks again; --Meena On Fri, Dec 14, 2018 at 5:59 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > 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.g...@yale.edu > > Tel:(203)903-4334 > > > > > > > > On Dec 14, 2018, at 10:53 AM, Bruce Fischl < > fis...@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&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.ox.ac.uk%2Fcrystal%2Fl > > 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.g...@yale.edu > > Tel:(203)903-4334 > > > > > > > > On Dec 13, 2018, at 3:49 PM, Bruce Fischl < > fis...@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 > > > > > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- — *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Yale University School of Medicine <http://people.yale.edu/search/meena_beshara.profile> Postdoctoral Associate | The John B. Pierce Laboratory <http://jbpierce.org/postdoctoral-associates/> Postdoc Committee Chair | The John B. Pierce Laboratory <http://jbpierce.org/postdoctoral-associates/> Career Development and Mentoring Manager Elect | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449> 290 Congress Avenue, New Haven, CT 06519 +1 (475) 731-5592 <+1%20475-731-5592>
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