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

 

 

 

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

        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

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