Hi Anna.
well, what's echoed in the terminal does matter :-)... It's presumably telling you that all images are segmented, then that the spatial transformations are estimated for all of them, which is fine. These transformations will *only be applied* to the images contained in the template_list file if there is such text file in your fslvbm directory, otherwise to all of them.
Just check (either with fslview of fslinfo) that your template_4D_GM only has the right number of subjects.
Cheers,
Gwenaelle
--- En date de : Ven 3.4.09, Anna Barnes <[log in to unmask]> a écrit :
> De: Anna Barnes <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] fslvbm_2_template does not read template file
> À: [log in to unmask]
> Date: Vendredi 3 Avril 2009, 13h14
> Hi Gwenaelle,
> I thought I had. My template_list file has a list of the
> subsample in the form filename.nii.gz. When I run
> fslvbm_2_template a list of names (e.g filename_struc) is
> echoed to the terminal window and I checked it against the
> template_list file and it's not the same. I feel I must
> be missing something very obvious :), may be it doesn't
> matter what gets echoed to the terminal window..
> thanks
> Anna
> --
> Anna Barnes, PhD
> Research Associate (+441223 764676)
>
> Brain Mapping Unit (Sir William Hardy Bldg.)
> Dept. of Psychiatry.
> c/o Experimental Psychology
> University of Cambridge.
> Downing Site, Downing St.
> Cambridge, CB2 3EB
>
>
>
>
>
> On 3 Apr 2009, at 11:34, Gwenaëlle DOUAUD wrote:
>
> > Hi Anna,
> >
> > so you mean the template is created with all your
> images instead of a balanced (between groups) subsample of
> them?
> > What you did looks fine to me... You should run all
> the fslvbm command from your my_fsl_vbm/ directory. Did you
> create the template_list file as indicated in the manual
> A.b)?
> >
> > Cheers,
> > Gwenaelle
> >
> >
> > --- En date de : Ven 3.4.09, Anna Barnes
> <[log in to unmask]> a écrit :
> >
> >> De: Anna Barnes <[log in to unmask]>
> >> Objet: [FSL] fslvbm_2_template does not read
> template file
> >> À: [log in to unmask]
> >> Date: Vendredi 3 Avril 2009, 11h30
> >> Hi I just read this post
> >>
> >> "Hi - please see the manual:
> >> http://fsl.fmrib.ox.ac.uk/fsl/fslvbm/#prepare
> >> You need to create this file in the study working
> >> directory, i.e. one
> >> level above FAi. Note also that the image names
> need to be
> >> the
> >> original names, without the _FAi in them."
> >>
> >> And so I think I have configured my directory
> structure
> >> properly but I still find that
> >> fslvbm_2_template just reads in all files from my
> working
> >> directory rather than what is
> >> specified in the template_list file.
> >>
> >> In my_fsl_vbm directory I have all my original
> files, a
> >> directory called struc with the
> >> fslvbm_1_bet -N output, a directory called
> slicedir and my
> >> template_list file.
> >>
> >> So in this situation where should my template_list
> file be
> >> and which directory should I be
> >> running fslvbm_2_template from.
> >>
> >> Thanks for listening
> >> Anna
> >
> >
> >
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