Thanks, Doug.

 

How would I go about getting the partial EPI to register with the T1? You can see in my previous emails, I just haven’t been able to get this to work. I have been using the –feat flag, can I still use this?

Any help on this would be great.

 

Sorry, I am just unsure with the possible flag combinations.

 

 

 

yes, sometimes it will  work ok and sometimes it won't. Partial FoV registration to a whole brain can be finicky. But if it works, then nothing wrong with it.

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I am really not sure, sorry. This is a secondary data set that I am using, I didn’t collect these data. For a number of the PPTS, there is no whole brain volume. Which is why I wondered if I could get a good registration without it. For 3/10 it worked fine as I was just running:

 

bbregister --s PPT_001 --feat /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/ --init-coreg

 

As you can see, the whole brain and T1 registered well with the second command you sent. Is there a way I can do something similar with just the partial FOV epi?

 

Thanks for your help with this.

 

 

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: Wednesday, 3 June 2020 at 17:45
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

 

You can ignore that warning. The source of the problem is that the whole-brain and the partial FoV are not in alignment. The idea here is that you acquire the whole head and the partial fov in the same scanning session so that they are more-or-less in alignment. When you register the whole brain to the structural, you can then get the partial fov to structural by concatenating the registrations. So, why is your whole brain out of alignment with the partial fov?

On 6/3/2020 12:31 PM, Mason Wells wrote:

        External Email - Use Caution        

Hi Doug,

 

Do you mean to raw partial epi and the whole brain? If so, I have ran:

tkregisterfv --mov /home/c1749990/data/PhD/Data/PMA_retinoScans/PPT_002/run1.nii.gz --targ /home//c1749990/data/PhD/Data/PMA_retinoScans/PPT_002/WholeEPI.nii.gz --regheader --reg partial-to-full.lta

 

but the once Freeview opens, the terminal states:

 

Warning: Transformation can only apply to volumes for now. If your data includes ROI/Surface/Way Points, please do not use this feature yet.

INFO: LTA input is not RAS to RAS...converting...

 

Also, in the freeview window, the whole brain and the raw epi are very misaligned as I click between displaying the two volumes in Freeview (attached). I should also add, of the 10 I have ran I did not use the whole brain –int flag as it appeared to make the registration a lot worse than just running:

 

bbregister --s PPT_002 --feat /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_002/run1.feat/ --init-coreg

 

Should I still try and register the whole epi to the T1 (structural)?

 

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: Wednesday, 3 June 2020 at 17:14
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

 

A couple of things to try:

First, make sure that the whole head and the partial FoV EPIs are in register without doing any registration
tkregisterfv --mov partialfovepi.nii.gz --targ wholeepi.nii.gz --regheader --reg partial-to-full.lta

Next, register the whole head EPI to the structural
bbregister --mov wholeepi.nii.gz --s subject --t2 --reg whole-to-struct.lta
View the result and make sure that it is in register

Let me know how that goes

On 6/3/2020 11:33 AM, Mason Wells wrote:

        External Email - Use Caution        

Sorry for yet another email on this, but 3/10 PPTs ended up with a good reg from bbregister, all using the same command. The issue is always when the epi orientation is like the attached. Have you any idea what to do? It's almost like bbregister can't orientate the brain so the epi is in the plane as the white matter. An epi slice is diagonal and the structural slice is horizontal, and this is where the issue is.

 

Cheers,

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

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.uk>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 3 June 2020 at 14:05
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

 

        External Email - Use Caution        

Hi Doug,

 

Thanks for this. However, I can’t seem to access the ftp:

 

c1749990@l017:~/data/freesurfer/subjects$ ftp surfer.nmr.mgh.harvard.edu

bash: ftp: command not found...

 

Is there another way to do this?

Cheers,

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

 

 

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: Tuesday, 2 June 2020 at 18:39
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

 

If you upload the data, I'll take a look. Upload both the structural and the fMRI. See instructions below

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.

On 6/2/2020 9:14 AM, Mason Wells wrote:

        External Email - Use Caution        

Just a follow up here. I tried the command below on a machine with v.6, and the flag was recognised, but the registration was still off. No change to the output with the flag included.

 

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 Mason Wells <WellsMT1@cardiff.ac.uk>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 2 June 2020 at 14:06
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

 

        External Email - Use Caution        

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?

 

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: Tuesday, 2 June 2020 at 13:48
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

 

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.

On 6/2/2020 6:40 AM, Mason Wells wrote:

        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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