Hi Matthew,
just off the top of my head, the only thing I can think of is a problem we had a while ago with people using ubuntu. If you're one of them, either try to update your version of FSL, or a simple fix is to replace the function "imglob" by "remove_ext" in the script (try this anyway)...
I can't check right now, but I suspect removing the _brain extension in the script would lead to something not quite right.
Let me know if the quick fix works.
Cheers,
Gwenaëlle
--- En date de : Jeu 10.12.09, Matthew Hoptman <[log in to unmask]> a écrit :
> De: Matthew Hoptman <[log in to unmask]>
> Objet: [FSL] fslvbm_2_template
> À: [log in to unmask]
> Date: Jeudi 10 Décembre 2009, 20h27
> Hi
> I had a question regarding fslvbm_2_template step of
> FSL-VBM
>
> I ran fslvbm_1_bet on images named like *mprr.nii.gz" and
> then put the images
> I needed for the template into template_list.
> Template list was the list of
> original files (*mprr.nii.gz")
>
> I then ran fslvbm_2_template on those images and it
> bombed. In the "struc"
> directory created in the first step, I got a series of
> files, but the ones I
> needed were named like
> "*mprr.nii.gz_struc.nii.gz_brain.nii.gz".
>
> However, in looking at fslvbm2a in the struc directory, I
> see that the program
> was looking for files like
> "*mprr.nii.gz_struc.nii.gz_brain.nii.gz_brain.nii.gz".
>
> Those didn't exist.
>
> I got the program to work by removing the "_brain" from
> line 99 of the
> fslvbm_2_template file, but did I do something wrong in the
> first place?
>
> Best,
> Matt
>
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