[JonatanSnir]

With respect to item #9, can I import data files after preprocessing with FSL – this would include BET, Eddy current corrections, registration to standard space, TBSS, DTIFIT, BEDPOSTX etc.. I hear great things about the brainsuite and would very much like to use it. If there is a proper way to prepare the output data from FSL preprocessing pipeline to fit the use of BDP could you please direct me to the instructions?
Thanks kindly,
Jon

[sychoi]

Sorry for the late response.

It depends on which components you want to you FSL for and which components you want to you BDP for.

Of the things you named, I would suggest only running the eddy current correction and then you can use that output from FSL as your input for BDP.

[micaceous]

Hello,

Following the co-reg of diffusion space to T1 space, are the bvectors reoriented in proportion to the degree of deformation?

Thank you,
Micah

[Anonymous]

Following the co-reg of diffusion space to T1 space, are the bvectors reoriented in proportion to the degree of deformation?

When transferring diffusion data to T1-space, b-vectors are reoriented using the computed rigid mapping between the spaces. The non-rigid EPI deformation (used for distortion-correction) of the diffusion data does not affect diffusion encoding directions, hence is not used for reorientation of b-vectors.

[micaceous]

Perfect, thank you!

[micaceous]

I just realized that Bhushan et al. (2012) is your manuscript, very cool, I enjoyed reading it! I’m curious to know, because I don’t quite understand everything in it…given that, in my current situation, the voxel size transformation going from larger DWI (1x1x2mm) to smaller T1 (1x1x1mm) practically doubles the in-plane resolution of DWI, does the interpolation essentially create new diffusion data that didn’t exist before? If so, how does it do that? (sorry I know that’s a vague question, but perhaps there’s a paper you could point me to?). I’m guessing it doesn’t duplicate the information in a single 2mm DWI slice into the two 1mm T1 slices right?

I’m wondering this because I’ve always previously performed tractography and analysis in native diffusion space, and so I’m curious to know how doing it in native T1 space will affect it. Perhaps there are some specific disadvantages or trade-offs? But even if so, I have such bad distortion in this dwi data (and I have no field map or double acquisition), that I think BrainSuite’s method will confer substantial improvement.

[jottino]

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!!

[jacksoncole1122]

BDP supports NIfTI and limited DICOM input formats, with specific requirements for gradient directions and merged datasets. Like eBook writing, success depends on using the right formats, structure, and tools for optimal results.

[Author]

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