External Email - Use Caution
Hi again experts,
Sorry for several posts on this topic.
Of the three brains I have analysed using bbregister, one of them is very misaligned. However, the FSL alignment looks fine. I ran FAST segmentation to get the white matter (pv_2) and overlaid this onto the example_func2highres.nii (see left side of attached image). However, when I view the results of bbregister (for which I used the command bbregister --s S3 --feat /Data/Feat2/S3/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/) using tkregisterfv and anat2exf.register.dat, the output is misaligned (see right of attached image).
Is there a way to use the successful FSL transformation in Freesurfer, or is there any advice for correcting this misalignment?
Best wishes, Mason
Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK
Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage 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 Ffôn: 02920 879628
With a partial field of view functional volume, you need to do something special. If the functional was acquired in the same session as the anatmomical, you can try add --init-header *AFTER* --feat
On 4/20/2020 8:11 AM, Mason Wells wrote:
External Email - Use CautionHi again experts,
Sorry for several posts on this topic.
Of the three brains I have analysed using bbregister, one of them is very misaligned. However, the FSL alignment looks fine. I ran FAST segmentation to get the white matter (pv_2) and overlaid this onto the example_func2highres.nii (see left side of attached image). However, when I view the results of bbregister (for which I used the command bbregister --s S3 --feat /Data/Feat2/S3/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/) using tkregisterfv and anat2exf.register.dat, the output is misaligned (see right of attached image).
Is there a way to use the successful FSL transformation in Freesurfer, or is there any advice for correcting this misalignment?
Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <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 Ffôn: 02920 879628
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Douglas,
Thanks for the email back. I have added --init-header after --feat /Data/Feat2/S3/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/). It seems to have done the trick (see attached).
Is there a reason why I did not need this step with the other two subjects? Both these subjects also had a partial FOV functional. Would you recommend add this initialisation and rerun the other two subjects through bbregister?
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.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: Monday, 20 April 2020 at 17:52 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Misalignment following bbregister
With a partial field of view functional volume, you need to do something special. If the functional was acquired in the same session as the anatmomical, you can try add --init-header *AFTER* --feat On 4/20/2020 8:11 AM, Mason Wells wrote:
External Email - Use Caution
Hi again experts,
Sorry for several posts on this topic.
Of the three brains I have analysed using bbregister, one of them is very misaligned. However, the FSL alignment looks fine. I ran FAST segmentation to get the white matter (pv_2) and overlaid this onto the example_func2highres.nii (see left side of attached image). However, when I view the results of bbregister (for which I used the command bbregister --s S3 --feat /Data/Feat2/S3/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/) using tkregisterfv and anat2exf.register.dat, the output is misaligned (see right of attached image).
Is there a way to use the successful FSL transformation in Freesurfer, or is there any advice for correcting this misalignment?
Best wishes,
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 webpage https://www.cardiff.ac.uk/people/research-students/view/974214-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.ukmailto:WellsMT1@caerdydd.ac.uk
Ffôn: 02920 879628
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The partial FoV is tricky. Sometimes the volume-based registration (the initialization for bbregister) works ok and sometimes it does not. If your other two cases have a good final registration, then no need to re-run
On 4/20/2020 1:09 PM, WellsMT1@cardiff.ac.uk wrote:
External Email - Use Caution
Hi Douglas,
Thanks for the email back. I have added --init-header after --feat/Data/Feat2/S3/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/). It seems to have done the trick (see attached).
Is there a reason why I did not need this step with the other two subjects? Both these subjects also had a partial FOV functional. Would you recommend add this initialisation and rerun the other two subjects through bbregister?
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.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: *Monday, 20 April 2020 at 17:52 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Misalignment following bbregister
With a partial field of view functional volume, you need to do something special. If the functional was acquired in the same session as the anatmomical, you can try add --init-header *AFTER* --feat
On 4/20/2020 8:11 AM, Mason Wells wrote:
External Email - Use Caution Hi again experts, Sorry for several posts on this topic. Of the three brains I have analysed using bbregister, one of them is very misaligned. However, the FSL alignment looks fine. I ran FAST segmentation to get the white matter (pv_2) and overlaid this onto the example_func2highres.nii (see left side of attached image). However, when I view the results of bbregister (for which I used the command bbregister --s S3 --feat/Data/Feat2/S3/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/) using tkregisterfv and anat2exf.register.dat, the output is misaligned (see right of attached image). Is there a way to use the successful FSL transformation in Freesurfer, or is there any advice for correcting this misalignment? Best wishes, 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-> <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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7C5cbe0bb2058240bd7c5908d7e54b2a18%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637229983304643310&sdata=ctloPP2q%2BwElHAkR4RDB3YsHhdIKiiveAkTbC5cc1Xc%3D&reserved=0>
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