Hello fsl users,
I want to ask the same question that i've done one month ago, but for the
newer version of FSL 4.1 this time.
How can I avoid the first step of VBM analysis (fslvbm_1_bet) on FSL 4.1
since i have my data already "beted" from a previous analysis step?
Gwenaelle gave me an answer (it is attached in the end of this e-mail) that
worked fine with fsl 4.0.4 but since now i've upgraded fsl to 4.1 i have the
same problem again.
Thank you once more
On Mon, 21 Jul 2008 14:20:23 +0000, Gwenaëlle DOUAUD
<[log in to unmask]> wrote:
>Hi Antonios,
>
>absolutely. The only thing that is required is to present the data as if
they'd been processed in the right order...
>
>If, say, you've named your various brain extracted exams:
exam00X_brain.nii.gz, then after running tbss_1_preproc, you'll have in your
FAi/ directory all your images called exam00X_brain_FAi.hdr and .img.
>
>So you then just need to rename them exam00X_FAi_brain.hdr and .img.
>
>One additional requirement (for nomenclature purposes) is that you need to
have in your FAi/ directory corresponding files *without* the _brain suffix,
so in this case: exam00X_FAi.hdr and .img (no matter what they are, so for
you, empty files would just be fine: touch exam00X_FAi.hdr and .img).
>
>Hope this makes sense,
>Gwenaelle
>
>
>--- En date de : Lun 21.7.08, Antonios - Constantine Thanellas
<[log in to unmask]> a écrit :
>
>> De: Antonios - Constantine Thanellas <[log in to unmask]>
>> Objet: [FSL] following different order on VBM analysis steps
>> À: [log in to unmask]
>> Date: Lundi 21 Juillet 2008, 12h23
>> Dear fsl users,
>>
>> I want to analyse my data (controls-patients) using
>> fsl's VBM.
>>
>> All my data (whole heads) have been brain extracted with
>> BET beforehand in
>> another analysis part.
>>
>> So instead of "beting" my data again (2nd step of
>> VBM analysis) can i just
>> modify the already extracted brains with tbss_1_preproc
>> (1st step of VBM
>> analysis) and omit the second step?
>>
>> Thank you in advance
>> Antonios-Konstantinos Thanellas
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