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 fischl@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.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 weexamine the volume
of the left and right accumbens. In the UK BioBank data >20Ksubjects freesurfer
segmentations the left accumbens is clearly significantly largerthan the right
accumbens (https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu...
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...
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 usedfreesurfer and
found left accumbens > right. In our hands, and in 2 differentdata sets
collected in two different sites, we obtain the opposite withFreeSurfer (right
accumbens > left accumbens). Furthermore, when we segment these same data sets with FIRST fromFSL we do obtain
Left accumbens > right Accumbens in both data sets in agreementwith 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 ofMedicine
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