Sorry yes it was late and after all I'm getting married on Saturday so
a little distracted. ;-). Yes of course Matt's right: eddycorrect
then bet (on b0) then dtifit. Cheers
--------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington,
Oxford. OX3 9 DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask]
http://www.fmrib.ox.ac.uk/~steve
----------------------
On 19 Aug 2008, at 01:24, Matt Glasser <[log in to unmask]> wrote:
> I didn't see Steve's reply, but I'm also sure he didn't mean to say
> to run
> DTIFIT before BET, as a brain mask from BET is one of the inputs for
> DTIFIT.
> :)
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Steve Smith
> Sent: Monday, August 18, 2008 2:51 PM
> To: [log in to unmask]
> Subject: Re: [FSL] FLIRT co-registration of DWI dataset
>
> Hi - you should in general align all the different directions and b-
> values to each other, and run dtifit, before running BET.
> Cheers.
>
>
> On 18 Aug 2008, at 20:04, Megan Herting wrote:
>
>> Hi. I was trying to prepare my data for dtifit and have seemed to
>> run into a
>> problem and was looking for some advice.
>>
>> I have 4 averages consisting of 1 b0 and 20 gradient directions
>> (b1000),
>> before averaging these together to make one large DWI 4D file, I was
>> looking
>> to strip each of the 4 b0 images (using BET), align each b0 image to
>> the first
>> b0 and then apply those parameters to the rest of the gradient
>> directions
>> (using FLIRT and applyxfm4D). (See script below).
>>
>> While BET seems to have correctly stripped each b0, after running
>> flirt to align
>> the b0 and apply it to the rest of the gradient directions, my
>> output file
>> (${subj}.${DTI}.FG.EC.CR.nii.gz) has large pieces of skull around
>> the frontal
>> lobe and even the eyesocket/ball, while the superior, posterior, and
>> inferior
>> brain areas seem to be fully stripped. Any ideas what I am doing
>> wrong, or
>> how to fix it?
>>
>> Thanks in advance!
>> -Megan
>>
>> Below is the part of my script I seem to be having trouble with...
>>
>>
>> foreach DTI ( ${runnames} )
>> echo +_+ "BET ${DTI}"
>> bet ./${subj}.${DTI}.FG.EC.nii.gz ./
>> ${subj}.${DTI}.FG.EC.STR.nii.gz -m -f 0.3
>> end
>>
>> #Co-register stripped averaged 1st b0 to stripped 2nd-4th averaged
>> b0s
>> foreach DTI ( ${DTIs[2]} ${DTIs[3]} ${DTIs[4]} )
>> echo +_+ "Coregister ${DTI} to ${DTIs[1]}"
>> flirt -in ${subj}.${DTI}.FG.EC.STR.nii \
>> -ref ./${subj}.${DTI[1]}.FG.EC.STR.nii.gz \
>> -omat ${DTI}.to.${DTIs[1]}
>> #Apply b0 co-registration parameters to the rest of the gradient
>> directions
>> applyxfm4D ./${subj}.${DTI}.FG.EC.nii.gz \
>> ./${subj}.${DTI[1]}.FG.EC.STR.nii.gz \
>> ./${subj}.${DTI}.FG.EC.CR.nii.gz \
>> ${DTI}.to.${DTIs[1]} -singlematrix
>> end
>>
>
>
> ---
> ---
> ---------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---
> ---
> ---------------------------------------------------------------------
>
