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 mailto:WellsMT1@cardiff.ac.uk

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214-

*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 mailto: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 <mailto:WellsMT1@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->

	

*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 <mailto:WellsMT1@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628



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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 mailto:WellsMT1@cardiff.ac.uk

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214-

*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 mailto: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 <mailto:WellsMT1@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->

	

*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 <mailto:WellsMT1@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" <dgreve@mgh.harvard.edu>
<mailto:dgreve@mgh.harvard.edu>
*Reply to: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, 1 June 2020 at 17:38
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu>
<mailto: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 <mailto:WellsMT1@cardiff.ac.uk>

    */Tel/*: 02920 879628

    */Web/*: Cardiff University webpage
    <https://www.cardiff.ac.uk/people/research-students/view/974214->

    	

    *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
    <mailto:WellsMT1@caerdydd.ac.uk>

    */Ffôn/*: 02920 879628




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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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 18:02 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 17:38 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

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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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 14:06 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 13:48 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 18:02 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 17:38 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

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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 mailto:WellsMT1@cardiff.ac.uk

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214-

*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 mailto: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 mailto:WellsMT1@cardiff.ac.uk

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214-

*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 mailto: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 <mailto:WellsMT1@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->

	

*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 <mailto:WellsMT1@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason
Wells <WellsMT1@cardiff.ac.uk> <mailto:WellsMT1@cardiff.ac.uk>
*Reply to: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Tuesday, 2 June 2020 at 14:06
*To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
<mailto: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 <mailto:WellsMT1@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->

	

*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 <mailto:WellsMT1@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" <dgreve@mgh.harvard.edu>
<mailto:dgreve@mgh.harvard.edu>
*Reply to: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Tuesday, 2 June 2020 at 13:48
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu>
<mailto: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 <mailto:WellsMT1@cardiff.ac.uk>

    */Tel/*: 02920 879628

    */Web/*: Cardiff University webpage
    <https://www.cardiff.ac.uk/people/research-students/view/974214->

    	

    *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
    <mailto:WellsMT1@caerdydd.ac.uk>

    */Ffôn/*: 02920 879628

    *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
    "Douglas N. Greve" <dgreve@mgh.harvard.edu>
    <mailto:dgreve@mgh.harvard.edu>
    *Reply to: *Freesurfer support list
    <freesurfer@nmr.mgh.harvard.edu>
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    *Date: *Monday, 1 June 2020 at 18:02
    *To: *"freesurfer@nmr.mgh.harvard.edu"
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    <freesurfer@nmr.mgh.harvard.edu>
    <mailto: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
        <mailto:WellsMT1@cardiff.ac.uk>

        */Tel/*: 02920 879628

        */Web/*: Cardiff University webpage
        <https://www.cardiff.ac.uk/people/research-students/view/974214->

        	

        *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
        <mailto:WellsMT1@caerdydd.ac.uk>

        */Ffôn/*: 02920 879628

        *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
        <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
        of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
        <mailto:dgreve@mgh.harvard.edu>
        *Reply to: *Freesurfer support list
        <freesurfer@nmr.mgh.harvard.edu>
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        *Date: *Monday, 1 June 2020 at 17:38
        *To: *"freesurfer@nmr.mgh.harvard.edu"
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        <freesurfer@nmr.mgh.harvard.edu>
        <mailto: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
            <mailto:WellsMT1@cardiff.ac.uk>

            */Tel/*: 02920 879628

            */Web/*: Cardiff University webpage
            <https://www.cardiff.ac.uk/people/research-students/view/974214->

            	

            *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
            <mailto:WellsMT1@caerdydd.ac.uk>

            */Ffôn/*: 02920 879628








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External Email - Use Caution

I’ve gone ahead and run: bbregister --mov /home/c1749990/data/PhD/Data/PMA_retinoScans/PPT_002/WholeEPI.nii.gz --s PPT_002 --t2 --reg /home/c1749990/data/PhD/Data/PMA_retinoScans/PPT_002/whole-to-struct.lta

Output in Freeview is attached. It looks like a good registration to me when I open it in Freeview, but again the same terminal message is below:

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...

I assume that message is nothing to worry about?

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto: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 17:32 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 14:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 18:39 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 14:06 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 13:48 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 18:02 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 17:38 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

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External Email - Use Caution

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 17:14 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 14:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 18:39 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 14:06 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 13:48 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 18:02 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 17:38 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

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External Email - Use Caution

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.

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: "Douglas N. Greve" dgreve@mgh.harvard.edu Date: Wednesday, 3 June 2020 at 18:11 To: Mason Wells WellsMT1@cardiff.ac.uk, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

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. On 6/3/2020 12:49 PM, Mason Wells wrote:

External Email - Use Caution 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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 17:45 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 17:14 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 14:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 18:39 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 14:06 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 13:48 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 18:02 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 17:38 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

There is nothing in bbr that will directly do this, but you can hack it.

Once you run flirt and get the .mat file, run tkregister2 --mov partial.nii.gz --targ whole.nii.gz --fslmat flirt.mat --reg partial-to-whole.dat --ltaout partial-to-whole.lta This will bring up a window where you can verify that the registration looks ok. Hit the "Save Reg" button. You don't have to do this everytime, but the first time it is a good idea. Once you have confidence, you can run tkregister2 with --noedit, and it will just return creating the .dat and .lta files

Run bbregister with  the whole brain epi to get an LTA file (eg, whole-to-struct.lta)

Now combine them with mri_concatenate_lta -subject subject partial-to-whole.lta whole-to-struct.lta partial-to-struct.init.lta

Verify that the reg looks ok wtih tkregister2 --mov partial.nii.gz  --reg junk.dat --lta partial-to-struct.init.lta

Then run bbr like bbregister --mov partial.nii.gz   --init-reg partial-to-struct.init.lta  -reg  partial-to-struct.lta --t2

On 6/3/2020 1:25 PM, Mason Wells wrote:

External Email - Use Caution

Just another point, Doug. The whole brain to partial epi registers fine in Feat. The alignment looks good. So, I guess I have two questions. Is there something in bbregister that can get the alignment of the partial and whole brain epi to match (as in Feat), and in the case where a whole brain isn’t acquired, what command/flags should be used in order to get the partial epi to align with the anatomical?

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 mailto:WellsMT1@cardiff.ac.uk

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214-

*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 mailto: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 18:20 *To: *"Douglas N. Greve" dgreve@mgh.harvard.edu, Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

*        External Email - Use Caution *

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.

*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 mailto:WellsMT1@cardiff.ac.uk

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214-

*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 mailto:WellsMT1@caerdydd.ac.uk

*/Ffôn/*: 02920 879628

*From: *"Douglas N. Greve" dgreve@mgh.harvard.edu *Date: *Wednesday, 3 June 2020 at 18:11 *To: *Mason Wells WellsMT1@cardiff.ac.uk, Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

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.

On 6/3/2020 12:49 PM, Mason Wells wrote:

*        External Email - Use Caution *

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 <mailto:WellsMT1@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->

	

*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 <mailto:WellsMT1@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" <dgreve@mgh.harvard.edu>
<mailto:dgreve@mgh.harvard.edu>
*Reply to: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, 3 June 2020 at 17:45
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu>
<mailto: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 <mailto:WellsMT1@cardiff.ac.uk>

    */Tel/*: 02920 879628

    */Web/*: Cardiff University webpage
    <https://www.cardiff.ac.uk/people/research-students/view/974214->

    	

    *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
    <mailto:WellsMT1@caerdydd.ac.uk>

    */Ffôn/*: 02920 879628

    *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
    "Douglas N. Greve" <dgreve@mgh.harvard.edu>
    <mailto:dgreve@mgh.harvard.edu>
    *Reply to: *Freesurfer support list
    <freesurfer@nmr.mgh.harvard.edu>
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    *Date: *Wednesday, 3 June 2020 at 17:14
    *To: *"freesurfer@nmr.mgh.harvard.edu"
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    <freesurfer@nmr.mgh.harvard.edu>
    <mailto: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
        <mailto:WellsMT1@cardiff.ac.uk>

        */Tel/*: 02920 879628

        */Web/*: Cardiff University webpage
        <https://www.cardiff.ac.uk/people/research-students/view/974214->

        	

        *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
        <mailto:WellsMT1@caerdydd.ac.uk>

        */Ffôn/*: 02920 879628

        *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
        <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
        of Mason Wells <WellsMT1@cardiff.ac.uk>
        <mailto:WellsMT1@cardiff.ac.uk>
        *Reply to: *Freesurfer support list
        <freesurfer@nmr.mgh.harvard.edu>
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        *Date: *Wednesday, 3 June 2020 at 14:05
        *To: *Freesurfer support list
        <freesurfer@nmr.mgh.harvard.edu>
        <mailto: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
        <mailto:WellsMT1@cardiff.ac.uk>

        */Tel/*: 02920 879628

        */Web/*: Cardiff University webpage
        <https://www.cardiff.ac.uk/people/research-students/view/974214->

        	

        *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
        <mailto:WellsMT1@caerdydd.ac.uk>

        */Ffôn/*: 02920 879628

        *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
        <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
        of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
        <mailto:dgreve@mgh.harvard.edu>
        *Reply to: *Freesurfer support list
        <freesurfer@nmr.mgh.harvard.edu>
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        *Date: *Tuesday, 2 June 2020 at 18:39
        *To: *"freesurfer@nmr.mgh.harvard.edu"
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        <freesurfer@nmr.mgh.harvard.edu>
        <mailto: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
            <mailto:WellsMT1@cardiff.ac.uk>

            */Tel/*: 02920 879628

            */Web/*: Cardiff University webpage
            <https://www.cardiff.ac.uk/people/research-students/view/974214->

            	

            *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
            <mailto:WellsMT1@caerdydd.ac.uk>

            */Ffôn/*: 02920 879628

            *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
            <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on
            behalf of Mason Wells <WellsMT1@cardiff.ac.uk>
            <mailto:WellsMT1@cardiff.ac.uk>
            *Reply to: *Freesurfer support list
            <freesurfer@nmr.mgh.harvard.edu>
            <mailto:freesurfer@nmr.mgh.harvard.edu>
            *Date: *Tuesday, 2 June 2020 at 14:06
            *To: *Freesurfer support list
            <freesurfer@nmr.mgh.harvard.edu>
            <mailto: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
            <mailto:WellsMT1@cardiff.ac.uk>

            */Tel/*: 02920 879628

            */Web/*: Cardiff University webpage
            <https://www.cardiff.ac.uk/people/research-students/view/974214->

            	

            *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
            <mailto:WellsMT1@caerdydd.ac.uk>

            */Ffôn/*: 02920 879628

            *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
            <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on
            behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
            <mailto:dgreve@mgh.harvard.edu>
            *Reply to: *Freesurfer support list
            <freesurfer@nmr.mgh.harvard.edu>
            <mailto:freesurfer@nmr.mgh.harvard.edu>
            *Date: *Tuesday, 2 June 2020 at 13:48
            *To: *"freesurfer@nmr.mgh.harvard.edu"
            <mailto:freesurfer@nmr.mgh.harvard.edu>
            <freesurfer@nmr.mgh.harvard.edu>
            <mailto: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
                <mailto:WellsMT1@cardiff.ac.uk>

                */Tel/*: 02920 879628

                */Web/*: Cardiff University webpage
                <https://www.cardiff.ac.uk/people/research-students/view/974214->

                	

                *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
                <mailto:WellsMT1@caerdydd.ac.uk>

                */Ffôn/*: 02920 879628

                *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
                <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on
                behalf of "Douglas N. Greve"
                <dgreve@mgh.harvard.edu>
                <mailto:dgreve@mgh.harvard.edu>
                *Reply to: *Freesurfer support list
                <freesurfer@nmr.mgh.harvard.edu>
                <mailto:freesurfer@nmr.mgh.harvard.edu>
                *Date: *Monday, 1 June 2020 at 18:02
                *To: *"freesurfer@nmr.mgh.harvard.edu"
                <mailto:freesurfer@nmr.mgh.harvard.edu>
                <freesurfer@nmr.mgh.harvard.edu>
                <mailto: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
                    <mailto:WellsMT1@cardiff.ac.uk>

                    */Tel/*: 02920 879628

                    */Web/*: Cardiff University webpage
                    <https://www.cardiff.ac.uk/people/research-students/view/974214->

                    	

                    *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
                    <mailto:WellsMT1@caerdydd.ac.uk>

                    */Ffôn/*: 02920 879628

                    *From:
                    *<freesurfer-bounces@nmr.mgh.harvard.edu>
                    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
                    on behalf of "Douglas N. Greve"
                    <dgreve@mgh.harvard.edu>
                    <mailto:dgreve@mgh.harvard.edu>
                    *Reply to: *Freesurfer support list
                    <freesurfer@nmr.mgh.harvard.edu>
                    <mailto:freesurfer@nmr.mgh.harvard.edu>
                    *Date: *Monday, 1 June 2020 at 17:38
                    *To: *"freesurfer@nmr.mgh.harvard.edu"
                    <mailto:freesurfer@nmr.mgh.harvard.edu>
                    <freesurfer@nmr.mgh.harvard.edu>
                    <mailto: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
                        <mailto:WellsMT1@cardiff.ac.uk>

                        */Tel/*: 02920 879628

                        */Web/*: Cardiff University webpage
                        <https://www.cardiff.ac.uk/people/research-students/view/974214->

                        	

                        *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
                        <mailto:WellsMT1@caerdydd.ac.uk>

                        */Ffôn/*: 02920 879628












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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

External Email - Use Caution

Also, when I try to check if the registration between the raw partial epi and whole brain volume are OK. Running this line:

tkregisterfv --mov /home/c1749990/data/PhD/Data/PMA_retinoScans/PPT_004/run1.nii.gz --targ /home/c1749990/data/PhD/Data/PMA_retinoScans/PPT_004/WholeEPI.nii.gz --regheader --reg partial-to-full.lta

I get this error: although it appears to be inconsistent with which PPTs this happens with: ltaReadRegisterDat: could not read /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_004/partial-to-full.ltaÂ

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto: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: Thursday, 4 June 2020 at 13:07 To: "Douglas N. Greve" dgreve@mgh.harvard.edu, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

External Email - Use Caution Hi Doug,

I really appreciate the advice here. I’ve tried running the first step, but when I use the fslmat flag and point to the example_func2inital_high res (e.g. pre-processed epi to whole brain volume matrix output by Feat), I get the error below. Am I supposed to be using this matrix or is –fslmat a flag to output a fsl matrix (that what it suggests on the bbregister wiki page).

tkregister2 --mov /home/c1749990/data/PhD/Data/PMA_retinoScans/PPT_010/run1_pre_processed_functional.feat/filtered_func_data.nii.gz --targ /home/c1749990/data/PhD/Data/PMA_retinoScans/PPT_010/WholeEPI.nii.gz --fslmat /home/c1749990/data/PhD/Data/PMA_retinoScans/PPT_010/run1_pre_processed_functional.feat/reg/example_func2initial_highres.mat --reg partial-to-whole.dat --ltaout partial-to-whole.lta tkregister_tcl /cubric/software/freesurfer.versions/6.0.0/tktools/tkregister2.tcl ERROR: Option --fslmat unknown

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: "Douglas N. Greve" dgreve@mgh.harvard.edu Date: Wednesday, 3 June 2020 at 22:09 To: Mason Wells WellsMT1@cardiff.ac.uk, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

There is nothing in bbr that will directly do this, but you can hack it.

Once you run flirt and get the .mat file, run tkregister2 --mov partial.nii.gz --targ whole.nii.gz --fslmat flirt.mat --reg partial-to-whole.dat --ltaout partial-to-whole.lta This will bring up a window where you can verify that the registration looks ok. Hit the "Save Reg" button. You don't have to do this everytime, but the first time it is a good idea. Once you have confidence, you can run tkregister2 with --noedit, and it will just return creating the .dat and .lta files

Run bbregister with the whole brain epi to get an LTA file (eg, whole-to-struct.lta)

Now combine them with mri_concatenate_lta -subject subject partial-to-whole.lta whole-to-struct.lta partial-to-struct.init.lta

Verify that the reg looks ok wtih tkregister2 --mov partial.nii.gz --reg junk.dat --lta partial-to-struct.init.lta

Then run bbr like bbregister --mov partial.nii.gz --init-reg partial-to-struct.init.lta -reg partial-to-struct.lta --t2

On 6/3/2020 1:25 PM, Mason Wells wrote:

External Email - Use Caution Just another point, Doug. The whole brain to partial epi registers fine in Feat. The alignment looks good. So, I guess I have two questions. Is there something in bbregister that can get the alignment of the partial and whole brain epi to match (as in Feat), and in the case where a whole brain isn’t acquired, what command/flags should be used in order to get the partial epi to align with the anatomical?

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 18:20 To: "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu, Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

External Email - Use Caution 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.

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Wednesday, 3 June 2020 at 18:11 To: Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk, Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

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. On 6/3/2020 12:49 PM, Mason Wells wrote:

External Email - Use Caution 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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 17:45 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 17:14 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 14:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 18:39 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 14:06 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 13:48 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 18:02 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 17:38 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

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External Email - Use Caution

Hi Doug,

This worked great for 9/10 participants. Thanks for your help!

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: "Douglas N. Greve" dgreve@mgh.harvard.edu Date: Wednesday, 3 June 2020 at 22:09 To: Mason Wells WellsMT1@cardiff.ac.uk, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

There is nothing in bbr that will directly do this, but you can hack it.

Once you run flirt and get the .mat file, run tkregister2 --mov partial.nii.gz --targ whole.nii.gz --fslmat flirt.mat --reg partial-to-whole.dat --ltaout partial-to-whole.lta This will bring up a window where you can verify that the registration looks ok. Hit the "Save Reg" button. You don't have to do this everytime, but the first time it is a good idea. Once you have confidence, you can run tkregister2 with --noedit, and it will just return creating the .dat and .lta files

Run bbregister with the whole brain epi to get an LTA file (eg, whole-to-struct.lta)

Now combine them with mri_concatenate_lta -subject subject partial-to-whole.lta whole-to-struct.lta partial-to-struct.init.lta

Verify that the reg looks ok wtih tkregister2 --mov partial.nii.gz --reg junk.dat --lta partial-to-struct.init.lta

Then run bbr like bbregister --mov partial.nii.gz --init-reg partial-to-struct.init.lta -reg partial-to-struct.lta --t2

On 6/3/2020 1:25 PM, Mason Wells wrote:

External Email - Use Caution Just another point, Doug. The whole brain to partial epi registers fine in Feat. The alignment looks good. So, I guess I have two questions. Is there something in bbregister that can get the alignment of the partial and whole brain epi to match (as in Feat), and in the case where a whole brain isn’t acquired, what command/flags should be used in order to get the partial epi to align with the anatomical?

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 18:20 To: "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu, Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

External Email - Use Caution 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.

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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Date: Wednesday, 3 June 2020 at 18:11 To: Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk, Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bbregister misalignment {Disarmed}

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. On 6/3/2020 12:49 PM, Mason Wells wrote:

External Email - Use Caution 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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 17:45 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 17:14 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 3 June 2020 at 14:05 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 18:39 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 14:06 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 2 June 2020 at 13:48 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 18:02 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, 1 June 2020 at 17:38 To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- 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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

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Use mri_vol2vol, eg, mri_vol2vol --mov filtered_func_data.nii.gz  --reg partial-to-struct.lta  –o ffd-struct.nii.gz --fstarg

On 6/18/2020 10:43 AM, Mason Wells wrote:

External Email - Use Caution

Hi Doug,

I have just one final question RE this registration pipeline. So far it’s worked great for 9/10 PPTs, so thanks. I assume there isn’t much I can do about the 1/10 participant? However, the original plan was to get this transformation matrix (partial-to-struct.lta) and use it in mri_vol2surf. However, if I want to just apply the final transformation to the filtered_func.nii.gz file, can I just simple run the following command with –o to apply the transformation directly to the filtered_func.nii.gz inside the bbregister command? Or will I have to take the partial-to-struct.lta and apply it in something like applyxfm?

bbregister --mov filtered_func_data.nii.gz --init-reg partial-to-struct.init.lta --reg partial-to-struct.lta --t2 –o

Thanks,

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 mailto:WellsMT1@cardiff.ac.uk

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214-

*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 mailto:WellsMT1@caerdydd.ac.uk

*/Ffôn/*: 02920 879628

*From: *"Douglas N. Greve" dgreve@mgh.harvard.edu *Date: *Wednesday, 3 June 2020 at 22:09 *To: *Mason Wells WellsMT1@cardiff.ac.uk, Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

There is nothing in bbr that will directly do this, but you can hack it.

Once you run flirt and get the .mat file, run tkregister2 --mov partial.nii.gz --targ whole.nii.gz --fslmat flirt.mat --reg partial-to-whole.dat --ltaout partial-to-whole.lta This will bring up a window where you can verify that the registration looks ok. Hit the "Save Reg" button. You don't have to do this everytime, but the first time it is a good idea. Once you have confidence, you can run tkregister2 with --noedit, and it will just return creating the .dat and .lta files

Run bbregister with  the whole brain epi to get an LTA file (eg, whole-to-struct.lta)

Now combine them with mri_concatenate_lta -subject subject partial-to-whole.lta whole-to-struct.lta partial-to-struct.init.lta

Verify that the reg looks ok wtih tkregister2 --mov partial.nii.gz  --reg junk.dat --lta partial-to-struct.init.lta

Then run bbr like bbregister --mov partial.nii.gz   --init-reg partial-to-struct.init.lta  -reg  partial-to-struct.lta --t2

On 6/3/2020 1:25 PM, Mason Wells wrote:

*        External Email - Use Caution *

Just another point, Doug. The whole brain to partial epi registers
fine in Feat. The alignment looks good. So, I guess I have two
questions. Is there something in bbregister that can get the
alignment of the partial and whole brain epi to match (as in
Feat), and in the case where a whole brain isn’t acquired, what
command/flags should be used in order to get the partial epi to
align with the anatomical?

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 <mailto:WellsMT1@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->

	

*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 <mailto:WellsMT1@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason
Wells <WellsMT1@cardiff.ac.uk> <mailto:WellsMT1@cardiff.ac.uk>
*Reply to: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, 3 June 2020 at 18:20
*To: *"Douglas N. Greve" <dgreve@mgh.harvard.edu>
<mailto:dgreve@mgh.harvard.edu>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

*        External Email - Use Caution *

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.

*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 <mailto:WellsMT1@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->

	

*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 <mailto:WellsMT1@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *"Douglas N. Greve" <dgreve@mgh.harvard.edu>
<mailto:dgreve@mgh.harvard.edu>
*Date: *Wednesday, 3 June 2020 at 18:11
*To: *Mason Wells <WellsMT1@cardiff.ac.uk>
<mailto:WellsMT1@cardiff.ac.uk>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed}

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.

On 6/3/2020 12:49 PM, Mason Wells wrote:

    *        External Email - Use Caution *

    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 <mailto:WellsMT1@cardiff.ac.uk>

    */Tel/*: 02920 879628

    */Web/*: Cardiff University webpage
    <https://www.cardiff.ac.uk/people/research-students/view/974214->

    	

    *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
    <mailto:WellsMT1@caerdydd.ac.uk>

    */Ffôn/*: 02920 879628

    *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
    "Douglas N. Greve" <dgreve@mgh.harvard.edu>
    <mailto:dgreve@mgh.harvard.edu>
    *Reply to: *Freesurfer support list
    <freesurfer@nmr.mgh.harvard.edu>
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    *Date: *Wednesday, 3 June 2020 at 17:45
    *To: *"freesurfer@nmr.mgh.harvard.edu"
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    <freesurfer@nmr.mgh.harvard.edu>
    <mailto: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
        <mailto:WellsMT1@cardiff.ac.uk>

        */Tel/*: 02920 879628

        */Web/*: Cardiff University webpage
        <https://www.cardiff.ac.uk/people/research-students/view/974214->

        	

        *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
        <mailto:WellsMT1@caerdydd.ac.uk>

        */Ffôn/*: 02920 879628

        *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
        <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf
        of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
        <mailto:dgreve@mgh.harvard.edu>
        *Reply to: *Freesurfer support list
        <freesurfer@nmr.mgh.harvard.edu>
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        *Date: *Wednesday, 3 June 2020 at 17:14
        *To: *"freesurfer@nmr.mgh.harvard.edu"
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        <freesurfer@nmr.mgh.harvard.edu>
        <mailto: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
            <mailto:WellsMT1@cardiff.ac.uk>

            */Tel/*: 02920 879628

            */Web/*: Cardiff University webpage
            <https://www.cardiff.ac.uk/people/research-students/view/974214->

            	

            *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
            <mailto:WellsMT1@caerdydd.ac.uk>

            */Ffôn/*: 02920 879628

            *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
            <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on
            behalf of Mason Wells <WellsMT1@cardiff.ac.uk>
            <mailto:WellsMT1@cardiff.ac.uk>
            *Reply to: *Freesurfer support list
            <freesurfer@nmr.mgh.harvard.edu>
            <mailto:freesurfer@nmr.mgh.harvard.edu>
            *Date: *Wednesday, 3 June 2020 at 14:05
            *To: *Freesurfer support list
            <freesurfer@nmr.mgh.harvard.edu>
            <mailto: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
            <mailto:WellsMT1@cardiff.ac.uk>

            */Tel/*: 02920 879628

            */Web/*: Cardiff University webpage
            <https://www.cardiff.ac.uk/people/research-students/view/974214->

            	

            *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
            <mailto:WellsMT1@caerdydd.ac.uk>

            */Ffôn/*: 02920 879628

            *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
            <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on
            behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
            <mailto:dgreve@mgh.harvard.edu>
            *Reply to: *Freesurfer support list
            <freesurfer@nmr.mgh.harvard.edu>
            <mailto:freesurfer@nmr.mgh.harvard.edu>
            *Date: *Tuesday, 2 June 2020 at 18:39
            *To: *"freesurfer@nmr.mgh.harvard.edu"
            <mailto:freesurfer@nmr.mgh.harvard.edu>
            <freesurfer@nmr.mgh.harvard.edu>
            <mailto: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
                <mailto:WellsMT1@cardiff.ac.uk>

                */Tel/*: 02920 879628

                */Web/*: Cardiff University webpage
                <https://www.cardiff.ac.uk/people/research-students/view/974214->

                	

                *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
                <mailto:WellsMT1@caerdydd.ac.uk>

                */Ffôn/*: 02920 879628

                *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
                <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on
                behalf of Mason Wells <WellsMT1@cardiff.ac.uk>
                <mailto:WellsMT1@cardiff.ac.uk>
                *Reply to: *Freesurfer support list
                <freesurfer@nmr.mgh.harvard.edu>
                <mailto:freesurfer@nmr.mgh.harvard.edu>
                *Date: *Tuesday, 2 June 2020 at 14:06
                *To: *Freesurfer support list
                <freesurfer@nmr.mgh.harvard.edu>
                <mailto: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
                <mailto:WellsMT1@cardiff.ac.uk>

                */Tel/*: 02920 879628

                */Web/*: Cardiff University webpage
                <https://www.cardiff.ac.uk/people/research-students/view/974214->

                	

                *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
                <mailto:WellsMT1@caerdydd.ac.uk>

                */Ffôn/*: 02920 879628

                *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>
                <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on
                behalf of "Douglas N. Greve"
                <dgreve@mgh.harvard.edu>
                <mailto:dgreve@mgh.harvard.edu>
                *Reply to: *Freesurfer support list
                <freesurfer@nmr.mgh.harvard.edu>
                <mailto:freesurfer@nmr.mgh.harvard.edu>
                *Date: *Tuesday, 2 June 2020 at 13:48
                *To: *"freesurfer@nmr.mgh.harvard.edu"
                <mailto:freesurfer@nmr.mgh.harvard.edu>
                <freesurfer@nmr.mgh.harvard.edu>
                <mailto: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
                    <mailto:WellsMT1@cardiff.ac.uk>

                    */Tel/*: 02920 879628

                    */Web/*: Cardiff University webpage
                    <https://www.cardiff.ac.uk/people/research-students/view/974214->

                    	

                    *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
                    <mailto:WellsMT1@caerdydd.ac.uk>

                    */Ffôn/*: 02920 879628

                    *From:
                    *<freesurfer-bounces@nmr.mgh.harvard.edu>
                    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
                    on behalf of "Douglas N. Greve"
                    <dgreve@mgh.harvard.edu>
                    <mailto:dgreve@mgh.harvard.edu>
                    *Reply to: *Freesurfer support list
                    <freesurfer@nmr.mgh.harvard.edu>
                    <mailto:freesurfer@nmr.mgh.harvard.edu>
                    *Date: *Monday, 1 June 2020 at 18:02
                    *To: *"freesurfer@nmr.mgh.harvard.edu"
                    <mailto:freesurfer@nmr.mgh.harvard.edu>
                    <freesurfer@nmr.mgh.harvard.edu>
                    <mailto: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
                        <mailto:WellsMT1@cardiff.ac.uk>

                        */Tel/*: 02920 879628

                        */Web/*: Cardiff University webpage
                        <https://www.cardiff.ac.uk/people/research-students/view/974214->

                        	

                        *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
                        <mailto:WellsMT1@caerdydd.ac.uk>

                        */Ffôn/*: 02920 879628

                        *From:
                        *<freesurfer-bounces@nmr.mgh.harvard.edu>
                        <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
                        on behalf of "Douglas N. Greve"
                        <dgreve@mgh.harvard.edu>
                        <mailto:dgreve@mgh.harvard.edu>
                        *Reply to: *Freesurfer support list
                        <freesurfer@nmr.mgh.harvard.edu>
                        <mailto:freesurfer@nmr.mgh.harvard.edu>
                        *Date: *Monday, 1 June 2020 at 17:38
                        *To: *"freesurfer@nmr.mgh.harvard.edu"
                        <mailto:freesurfer@nmr.mgh.harvard.edu>
                        <freesurfer@nmr.mgh.harvard.edu>
                        <mailto: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
                            <mailto:WellsMT1@cardiff.ac.uk>

                            */Tel/*: 02920 879628

                            */Web/*: Cardiff University webpage
                            <https://www.cardiff.ac.uk/people/research-students/view/974214->

                            	

                            *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
                            <mailto:WellsMT1@caerdydd.ac.uk>

                            */Ffôn/*: 02920 879628













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