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

Email: WellsMT1@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

E-bost: WellsMT1@caerdydd.ac.uk

Ffôn: 02920 879628