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
