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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