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
    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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