External Email - Use Caution group cc'd - thanks for the reminder.
My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all? (Assuming that I can't just switch lh_ and rh_ in the aparcstats2table) Ellen On 9/15/2020 6:51 PM, Fischl, Bruce wrote: > Hi Ellen > > Can you cc the list so that others can respond? What was your input data? Did > you not have dicoms? > > Cheers > Bruce > > -----Original Message----- > From: Ellen Ji <ellen...@bli.uzh.ch> > Sent: Tuesday, September 15, 2020 12:38 PM > To: Fischl, Bruce <bfis...@mgh.harvard.edu> > Subject: Re: [Freesurfer] left-right flip? > > External Email - Use Caution > > Hi Bruce, > > Unfortunately I just found the fiducial and realised that the L-R is > incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table > or do I need to run mri_convert on the nifti and run recon-all from the > beginning again? > > Thanks, > > Ellen > > On 9/15/2020 5:44 PM, Fischl, Bruce wrote: >> 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 > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Mass General Brigham > Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If > the e-mail was sent to you in error but does not contain patient information, > please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
