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Dear Douglas,
Thank you for your reply.
Apologies, we actually do run the bbregister command, not fslregister, as follows: bbregister --s "${FSDIR}" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" --dti --init-fsl
We use FreeSurfer version 7.1.1, and I'm just now reading in the release notes of version 6.0: "bbregister now uses the FS mri_coreg program by to initialize BBR. FSL or SPM/matlab are no longer needed. mri_coreg is based on spm_coreg and gives very similar results as to when spmregister is run."
Does that mean the "--init-fsl" option is completely redundant? And could the warning message have been caused by using that option?
Kind regards, Simon ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: Tuesday, February 9, 2021 3:51 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslregister - WARNING: possible left-right reversal (image-heavy e-mail)
It looks ok to me. Why are you using fslregister? it is kind of depricated. use mri_coreg or, even better, bbregister
On 2/5/2021 10:13 AM, S.R. Poortman wrote:
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Dear sir/madam,
When running fslregister as part of our data (pre)processing steps, it consistently outputs the following warning:
[cid:part1.CA36D320.8525613E@mgh.harvard.edu]
This the mri_info --orientation output:
raw T1-weighted image: [cid:part2.6C69F4D2.3DDF351B@mgh.harvard.edu]
orig.mgz: [cid:part3.172726D6.9558EE74@mgh.harvard.edu]
However, when I look at all the images, raw and processed, I see no discrepancies with respect to orientation. See the images below. For reference, encircled in red, is the vitamin pill we stuck to the right side of the participant's forehead. Apologies for the image-heavy e-mail. I want to be thorough in providing enough information.
[cid:part4.6DD95C94.8DBD2D4F@mgh.harvard.edu] [cid:part5.16512999.E46A74F9@mgh.harvard.edu] [cid:part6.C2370B33.4A972A08@mgh.harvard.edu] [cid:part7.7968294B.38F2221E@mgh.harvard.edu] [cid:part8.C2BDD6A1.B3183D08@mgh.harvard.edu] [cid:part9.2308F35F.4E605796@mgh.harvard.edu] [cid:part10.B1E579CF.C75DDDD5@mgh.harvard.edu] [cid:part11.35FCDDCC.0B5CFA0C@mgh.harvard.edu]
Am I overlooking something, perhaps? Or does this warning also appear when nothing is wrong with the orientation(s) (the "possible" does seem to imply so)? Is there another way for me to make absolutely sure the orientations are correct and consistent?
Thank you for considering my questions.
Kind regards, Simon Poortman (Erasmus MC, Rotterdam)
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