Hi,
You can run BBR without fieldmaps, though not through the GUI. You need to do it separately using the script epi_reg. However, without fieldmaps you will not be correcting for the EPI distortions.
The alternative to having a fieldmap is to have a blip-up-blip-down (also called phase-encode reversed) set of b=0 (diffusion) images. These can be used with the tool topup to correct for distortions.
All the best,
Mark
> On 31 Dec 2016, at 11:21, Zeinab Gharaylou <[log in to unmask]> wrote:
>
> Dear Dr. Emmanuel,
> we have not a field map for using BBR cost function.
> Is there any way for registration?
>
> regards
>
>
> Zeinab Gharaylou
>
> Ph.D. Candidate of NeuroscienceTehran University of Medical Sciences
> Tehran, Iran
> Email: [log in to unmask]
>
>
> --------------------------------------------
> On Mon, 12/12/16, Emmanuel Vallee <[log in to unmask]> wrote:
>
> Subject: Re: [FSL] registration question
> To: [log in to unmask]
> Date: Monday, December 12, 2016, 2:55 PM
>
>
> Dear Zeinab,
>
>
> You need to register the mean B0
> (or S0) DWI image to the T1 image (in the space where the
> parcellation was performed).
> For this you can use flirt, with
> the BBR cost function. There is a script that performs the
> necessary step: epi_reg
> Please refer to the relevant FSL
> user guide page: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide#epi_reg.
> Do not hesitate to come back to
> us if you experience any issue or need further
> explanations.
>
>
>
> Cheers,
> Emmanuel
>
>
>
>
>
> On 12 Dec 2016, at 10:43, Zeinab
> Gharaylou <[log in to unmask]>
> wrote:
>
>
>
> Dear FSL experts,
>
>
>
> I am Ph.D. Candidate of Neuroscience. My thesis is
> regarding to quantitative analysis of DTI.I have some
> problem in registration of images. I want to register
> temporal lobe gray matter (achieved by parcellation of T1 by
> freesurfer) to FA map (achieved by
> camino and corrected by eddy fsl) with FSL. It would be
> appreciated if you let me know how I can perform it
> correctly. Which steps should be performed?
>
>
>
> regards
>
>
>
>
>
> Zeinab Gharaylou
>
>
>
> Ph.D. Candidate of NeuroscienceTehran University of Medical
> Sciences
>
> Tehran, Iran
>
> Email: [log in to unmask]
>
>
>
>
>
>
>
>
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