Hi Antonios-Constantine,
the problem here is that the extension of the images is not removed, but it's working fine for me. So what I would actually need is the content of your struc/ directory.
Cheers,
Gwenaelle
--- En date de : Sam 30.8.08, Antonios - Constantine Thanellas <[log in to unmask]> a écrit :
> De: Antonios - Constantine Thanellas <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] following different order on VBM analysis steps
> À: [log in to unmask]
> Date: Samedi 30 Août 2008, 20h15
> Hi Gwenaëlle,
>
> I have many errors when i'm running fslvbm_2_template
> -n
> The first one is :
>
> ** ERROR (nifti_image_read): failed to find header file for
> '01_CON_002_S_0295_M06_struc.nii.gz_brain'
>
> My files are of this form
> 01_CON_002_S_0295_M06_struc.nii.gz
>
> 02_CON_XXX__XXXXX_XXX_struc.nii.gz
> etc
> It seems that one of fsl scripts during the
> fslvbm_2_template run, adds this
> prefix { _brain} in the end of the file that should be
> read without renaming
> the actual file.So the script can't read a file that
> doesn't exist. Why this
> happens?
> I've noticed also that the names' files of some
> new created files are
> really strange with added big prefixes in the end of the
> file's name. For
> instance
> 01_CON_002_S_0295_M06_struc.nii.gz_GM_to_T_init_warp.msf
>
> I'm sending you the structure of my files in the folder
> where the analysis
> takes place+ the error messages that aroused during it.
>
> I would really appreciate once more your help
> Thank you
> Antonios-Constantine Thanellas
>
>
>
>
>
>
>
>
>
>
> On Tue, 26 Aug 2008 17:42:44 +0000, Gwenaëlle DOUAUD
> <[log in to unmask]> wrote:
>
> >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
> >>
> >>
> >>
> >>
> _____________________________________________________________________________
> >>
> >> Envoyez avec Yahoo! Mail. Une boite mail plus
> intelligente
> >> http://mail.yahoo.fr
>
>
>
> _____________________________________________________________________________
>
> Envoyez avec Yahoo! Mail. Une boite mail plus intelligente
> http://mail.yahoo.fr
