Hi Antonios,
now the pre-processed data are in a directory called struc/ (instead of FAi/).
You need to do exactly the same thing as previously, apart from the fact that there is no need for you to run tbss_1 anymore, and fnirt can deal with compressed nifti images (instead of analyze).
So it boils down to:
- rename your betted images: exam00X_struc_brain.nii.gz
- have in your struc/ directory corresponding files *without* the _brain suffix, so in this case: exam00X_struc.nii.gz (no matter what they are, so for you, empty files would just be fine: touch exam00X_struc.nii.gz).
Cheers,
Gwen
--- En date de : Lun 25.8.08, 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 25 Août 2008, 17h05
> 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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