And what is your input to recon-all? If it is dicom you should be pretty confident that we will get it correct
-----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 10:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip? How are you checking the LR orientation? On 9/15/2020 4:10 AM, Ellen Ji wrote: > External Email - Use Caution > > Dear experts, > > I recently performed recon-all on a set of subjects and the output > (aparcstats2table and asegstats2table) will be part of a meta-analysis of > other labs' cohorts. When assessing the asymmetry index direction (relative > size of left vs right hemisphere across multiple rois), our dataset shows an > inversion of the mean asymmetry index in several structures compared to the > other cohorts. > > For example, in our dataset, the lateral ventricle volume is on > average larger in the right hemisphere compared to the left, while the > opposite is true for all other cohorts. The same inversion of asymmetry is > visible in other structures that in general are more asymmetrical. > > In order to check this, I went through each T1 to make sure the orientation > was correct and indeed they are. > > Is there any possible way that there was a left-right inversion somewhere > during the recon-all pipeline? I want to make sure I did everything correctly > on our end and that the results are due to the biology and not a technical > mistake! > > I found this website on Left-right reversal, and it seems relevant to > my issue, but I'm not fully understanding what this means (how would > bias occur during segmentation?) - > https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal > > Many thanks for your input, > Ellen > > --- > > Ellen Ji, PhD > Postdoctoral Research Fellow > Psychiatric University Hospital > University of Zürich > ellen...@bli.uzh.ch > homanlab.github.io/ellen/ > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
