mri_convert --in_orientation LIA subject1.nii subject1_corrected.nii
Hi Ellen

Sorry to say it, but you really should start over. Not everything in the brain is bilaterally symmetric so processing and flipping won't be the same as flipping then processing.

Cheers
Bruce

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ellen Ji
Sent: Wednesday, September 16, 2020 3:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] left-right flip?

        External Email - Use Caution        

Hi Douglas,

I found the dicoms and confirm that the fiducial is on the opposite side relative to the nifti. Additionally, the PI just informed me that the fiducial was placed on the right side of the head and the nifti indicates left. I will enquire as to what method was used to convert from dicom as that appears to be the issue.

I already performed recon-all and aparcstats2table on the flipped nifti. 
Could you please advise if there is there an efficient way to deal with this or if I should start from the beginning?

Many thanks,

Ellen

On 9/15/2020 7:19 PM, Douglas N. Greve wrote:
First we have to determine whether it is really LR flipped or not. Do 
you still have the dicoms? If so, can you convert to mgz using 
mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see 
if the fiducial has changed sides relative to the nifti.
That is a fiducial. And do you know what side the fiducial was placed 
on? mri_info does not help. How did you convert from dicom?

ps. Please make sure to post to the list and not to us personally

On 9/15/2020 12:58 PM, Ellen Ji wrote:
          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 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-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 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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