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.ji@bli.uzh.ch Sent: Tuesday, September 15, 2020 12:38 PM To: Fischl, Bruce BFISCHL@mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
External Email - Use CautionHi 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 CautionDear 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.ji@bli.uzh.ch homanlab.github.io/ellen/
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