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
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