Hi,
If you are going to make your own bvecs then it is *very* important to understand our coordinate conventions, since you cannot rely on the “fast” voxel direction being treated equivalently when the determinant of the sform/qform matrix is positive versus negative. This is why we put this information on the website, as otherwise you would get inconsistent results using the NIFTI voxel coordinates (which align to the “fast” voxel direction straightforwardly) based on the handedness (radiological/neurological orientation, set by the determinant of the qform/sform matrix).
I hope this helps to make things clearer.
All the best,
Mark
> On 28 May 2019, at 14:51, Steven Tilley <[log in to unmask]> wrote:
>
> Thanks Mark,
>
> So if I were to make my own bvecs file, can I simple keep it consistent with the whatever data storage layout I choose (i.e., first vector component corresponds to the "fast" voxel direction, etc)?
>
> Thanks again
> Steve
>
> Steven Tilley, PhD
> Imaging Analyst
> Bloorview Research Institute
> 416 425 6220 x 3398
>
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
> Sent: Monday, May 27, 2019 6:48 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Question regarding bvecs
>
> CAUTION: This email originated from outside of the organization. Please do not click links or open attachments unless you are confident that the message is legitimate.
> ------------------------------------------------------------------------------
>
> Hi,
>
> You are right that all that matters is consistency.
> If you are getting your bvecs generated for you by some reconstruction tool (like dcm2nii) or from a pre-processed dataset then you need not worry about any of this. It is only really important if you are making your own bvecs (or using them outside of FSL) or if you are manipulating the image in some way (e.g. rotating it). For the latter we provide a utility called fdt_rotate_bvecs. If it is the former then you need to understand the details in the FAQ, as the voxel coordinates explained there are not the standard NIFTI voxel coordinates, and therefore have fixed handedness (the “radiological orientation”). It is mainly because of this internal convention (that you normally don’t have to worry about) that these things get a little confusing.
>
> All the best,
> Mark
>
>
>
>> On 27 May 2019, at 17:50, Steven Tilley <[log in to unmask]> wrote:
>>
>> Hello,
>>
>> I wanted to clarify my understanding of the bvecs file. This message [1] says that bvecs is in voxel coordinates. However, the FAQ [2] says that it assumes radological orientation. If it is truly in voxel coordinates, that it really shouldn't matter how the data is stored, so long as the two files are consistent, correct?
>>
>> 1. https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;f4c2eecb.06
>> 2. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/FAQ#What_conventions_do_the_bvecs_use.3F
>>
>> Thanks
>> Steve
>>
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