I think you're right - if BET is happy reading the 4D at all then yes
it will be using the first image for brain extraction, so yes this
will be the same as first separating out the B0 image - but you may as
well do that anyway, because you'll probably need it for registration
later.
Cheers.
On 13 Mar 2008, at 00:26, Deryk Beal wrote:
> Hello
>
> I use DTIStudio to convert my dicom images to a 4-D analyze and then
> run the 4-D images through Eddy Current Correct in FSL. Does anyone
> know if it is okay to use the .nii.gz file created after Eddy
> Current Correction to create the brain mask for DTIFIT in BET? The
> instructions for DTIFIT/TBSS preprocessing seem to imply that you
> must separate out the B0 volume as its own analyze file for use with
> BET. Is this really necessary? It seems that BET automatically uses
> the first volume from the .nii.gz file which is the B0. I compared
> the extracted brain and brain mask from running BET on the .nii.gz
> file and an extracted B0-alone analyze image to each other and the
> output appears the same. However, as I am new to FSL and DTI
> analysis I am wondering if there is something more to it that I may
> be overlooking.
>
> Thanks
>
> Deryk
>
>
> --
> Deryk Beal, M.HSc., S-LP(C), Reg. CASLPO
> Speech-Language Pathologist
> Doctoral Candidate
> 416-946-8635
> [log in to unmask] or [log in to unmask]
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