Hi Doug,

 

I have FS v6.0 and tried the following command:

 

ERROR: Flag --init-coreg unrecognized.

--s PPT_001 --feat /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/ --int /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz --init-header --init-coreg

 

Still get the error. Is this correct use of the flags?

 

 

 

Right now, I'm just guessing what the problem is (I'm speculating that it is FSL FLIRT). You could download just the new bbregister and mri_coreg to your VM and see if it works.

        External Email - Use Caution        

I am using version 5.3, this is the version on the virtual machine I am working from. I can ask about an updated version, but is there a way to fix this on v5.3 in the meantime?

 

Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff    CF24 4HQ UK   Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage

Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd    CF24 4HQ  DU   E-bost: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 1 June 2020 at 18:02
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

 

What version of FS are you running? That flag was introduced with v6

On 6/1/2020 12:57 PM, Mason Wells wrote:

        External Email - Use Caution        

Hi Doug,

 

That flag isn’t recognised in the terminal? Have I placed the flag in the wrong place? I tried it between the –feat and the directory, same outcome.

 

bbregister --s PPT_001 --feat /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/ --int /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz --init-header --init-coreg

 

ERROR: Flag --init-coreg unrecognized.

--s PPT_001 --feat /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_

 

Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff    CF24 4HQ UK   Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage

Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd    CF24 4HQ  DU   E-bost: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 1 June 2020 at 17:38
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment

 

Sorry for missing your first email. Can you try adding --init-coreg to your first bbregister command? Make sure to add it AFTER --feat

On 6/1/2020 12:06 PM, Mason Wells wrote:

        External Email - Use Caution        

Hi Experts,

 

I posted earlier, but I believe my message has not been posted due to the size of attachments so I’ve removed them.

 

I am using bbregister to align functional data to anatomical space. I have been using the bbregister command with a combination of different flags. However, there appears to be varying levels of poor registration. 

 

The first command I used included flags for a whole brain ref image and the --init-header flag. This leads to a misalignment.

 

bbregister --s PPT_1x --feat  /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/ --int  Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header

 

I then removed the –int (whole brain reg image) flag. Again the registration is massively misaligned.

 

bbregister --s PPT_1x --feat  /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat --init-header

 

I then removed the –init-header flag. Again poor registration.

 

Then I removed both flags. This was the best registration, but even this still looks a little bit off to me. You can see that around the occipital lobe (reg3 attached), there white matter isn't aligned very well.

 

bbregister --s PPT_1x --feat /Data/PPT_1x/run1_pre_processed_functional.feat/

 

Can anyone give me any advice on this? I really am unsure as to which why these flags failed to aid registration. I have 3 other participants from a different dataset for which the bbregister pointing to the feat directory and the –init-header flag worked perfectly. Have I missed an important step that could explain why no combination seems to register the data correctly?

 

Any advice would be great.

Thanks in advance,

Mason

 

 

Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff    CF24 4HQ UK   Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage

Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd    CF24 4HQ  DU   E-bost: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

 

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