jottino

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  • in reply to: bdp.sh is not working #1163
    jottino
    Participant

    hi,

    this is not working either for me.

    in reply to: BDP – Frequently Asked Questions #748
    jottino
    Participant

    hi!

    is it OK if I correct my dwi images for eddy currents in FSL, rotate my bvecs with fdt_rotate_bvecs.sh (FSL script) and then use that output (eddy corrected dwi volumes and rotated b-vecs) in BS-BDP for further processing?

    I read a response in this same thread that says that bvecs are rotated (again) when registered to the T1-weighted image (.bfc.nii.gz).

    Would my pipeline (FSL->BS) of preprocessing suppose any kind of problem? Thanks!!

    jottino
    Participant

    Hi!

    I’m starting with BS too because of the possibility of correcting EPI distortions with T1-weighted images.

    I used both the –dwi-mask and –t1-mask in order to improve the correction following your advice, but the outcome was pretty the same. In fact, the outcome was even worse when I used one (–dwi-mask) or both masks (dwi+t1) than when I did not use any of them.

    Maybe without a fieldmap and only a T1 little correction could be made? Don’t get me wrong, I’m quite glad with correcting at least a little of such distortions than leave my DWI volumes with such disturbances.

    Regards,
    Jonatan

Viewing 3 posts - 1 through 3 (of 3 total)