If you don't have a fiducial, then there is no way to know for sure; mri_info just gets the same info that freeview gets, which comes from the header. How did you convert the file from dicom?
On 9/15/2020 11:33 AM, Ellen Ji wrote:
External Email - Use Caution Oh no, then I guess we have to assume a fiducial wasn't used. Is there any other way to determine which is left and right? Does the LAS/ASR/PSR from mri_info tell us that at all?
Thanks,
Ellen
On 9/15/2020 5:23 PM, Douglas N. Greve wrote:
How do you know which side of the subject is left and right? I don't see a fiducial. You do not need to convert the orientation to RAS.
On 9/15/2020 10:29 AM, Ellen Ji wrote:
External Email - Use Caution I loaded each T1 into freeview and verified that what freeview thinks is left and right, and anterior and posterior, is also what I see. Attached is a screenshot.
However, when I ran "mri_info --orientation, the orientations of the subjects are either LAS or ASR and PSR (i.e. not consistent and not RAS). Is this going to affect the output of recon-all? Do I need to convert all the orientations to RAS before running recon-all?
Thanks,
Ellen
On 9/15/2020 4:17 PM, Douglas N. Greve wrote:
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.ji@bli.uzh.ch homanlab.github.io/ellen/
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