If you run the bet command you should not get much extra brain signals. As
for the BedpostX options, it is fine to leave them at the defaults.
Peace,
Matt.
-----Original Message-----
From: Alexander Lebedev [mailto:]
Sent: Tuesday, March 31, 2009 4:36 AM
To: [log in to unmask]
Subject: Re: [FSL] Some questions about DTI analysis
Hello Matt!
Thank you very much for your answer. Tell please what about extra-brain
signals on FA maps?
What exact variables I have to set in Advanced Options (BedpostX) in
"Fibres", "Weight", "Burnin". Is it ok to set them as defaults?
Images was taken from Siemens Magnetom Symphony 1.5 T in 12+1 directions
(b-values: 0 and 900)
Best Regards...
* Matt Glasser <[log in to unmask]> [Mon, 30 Mar 2009 19:37:31 -0500]:
> To get the b0:
>
> fslroi data nodif 0 1
>
> To get the mask:
>
> bet nodif nodif_brain -m -f 0.5
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Alexander Lebedev
> Sent: Monday, March 30, 2009 7:04 PM
> To: [log in to unmask]
> Subject: [FSL] Some questions about DTI analysis
>
> Dear FSL users. Excuse me for disturbing you. I have some questions
> about dti data analysis in FDT toolbox.
>
> Now I have 4d nii file with (+ 2 txt's: b-values and gradient
> directions) getting after the convertation process from 299 dicom
files
> (12+1 directions)
> I have finished the eddy current correction (reference vol: 0) process
> and now I'm starting the "DTIfit"
>
> I use the b0 image (raw, not corrected) as a nodif_brain_mask (is it
> ok?). And could you give me advice how could I correctly get 3d mask
> image from 4d nii? (It is probably due to my lack of experience...
> Sorry)
>
> And... There are many extra-brain signals in my FA-maps getting after
> the processing... Is it ok?
>
> P.S.: I've found the worm ("Scano.F") in the "FSL practicals" (3rd
> archieve)...
--
Alexander Lebedev.
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