Hi Aga,
this is not possible to have a template_GM created without the 4D_GM one. It must have been moved or deleted afterwards... You should also check that your template_GM is the most recent one (ls -al) and not one created a while ago.
Cheers,
Gwenaelle
--- En date de : Jeu 17.9..09, Agnieszka Burzynska <[log in to unmask]> a écrit :
> De: Agnieszka Burzynska <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] FSL-vbm: how do i know that template_list was read?
> À: [log in to unmask]
> Date: Jeudi 17 Septembre 2009, 16h55
> Dear Gwenaelle,
> Now the template_GM was created, but templte_4D_GM not, so
> i cannot check
> which and how many volumes are included in template
> creation.
>
> I will be very grateful for any further hint!
>
> Best,
> Aga
>
>
> On 9/17/09 12:43 PM, "Gwenaëlle DOUAUD" <[log in to unmask]>
> wrote:
>
> > Hi Aga,
> >
> > that's what I thought... The name of the template list
> has to be *exactly*
> > "template_list", and it has to be a text file,
> otherwise this is not recognise
> > by the script and therefore not taken into account
> :-)...
> >
> > Cheers,
> > Gwenaelle
> >
> > --- En date de : Jeu 17.9.09, Burzynska, Aga <[log in to unmask]>
> a
> > écrit :
> >
> >> De: Burzynska, Aga <[log in to unmask]>
> >> Objet: [FSL] AW: [FSL] Re : [FSL] AW: [FSL] Re :
> [FSL] FSL-vbm: how do i know
> >> that template_list was read?
> >> À: [log in to unmask]
> >> Date: Jeudi 17 Septembre 2009, 10h49
> >>
> >>
> >>
> >>
> >>
> >> AW: [FSL] Re : [FSL] AW: [FSL] Re : [FSL]
> FSL-vbm:
> >> how do i know that template_list was read?
> >>
> >>
> >>
> >>
> >> Yes, sure, here it is!
> >>
> >>
> >>
> >> best,
> >>
> >> Aga
> >>
> >>
> >>
> >> Aga Burzynska
> >>
> >> Max Planck Institute for Human Development
> >>
> >> Neurocognition of Decision Making
> >>
> >> Lentzeallee 94
> >>
> >> 14195 Berlin
> >>
> >> Ph: + 49 30 82406 335
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> -----Ursprüngliche Nachricht-----
> >>
> >> Von: FSL - FMRIB's Software Library im Auftrag
> von
> >> Gwenaëlle DOUAUD
> >>
> >> Gesendet: Mi 2009-09-16 18:27
> >>
> >> An: [log in to unmask]
> >>
> >> Betreff: [FSL] Re : [FSL] AW: [FSL] Re : [FSL]
> FSL-vbm: how
> >> do i know that template_list was read?
> >>
> >>
> >>
> >> Hi Aga,
> >>
> >>
> >>
> >> could you please attach your template_list file
> exactly as
> >> it is in your vbmAga directory?
> >>
> >>
> >>
> >> Cheers,
> >>
> >> Gwenaelle
> >>
> >>
> >>
> >> --- En date de : Mer 16..9.09, Burzynska, Aga
> >> <[log in to unmask]>
> a écrit :
> >>
> >>
> >>
> >>> De: Burzynska, Aga
> >> <[log in to unmask]>
> >>
> >>> Objet: [FSL] AW: [FSL] Re : [FSL] FSL-vbm: how
> do i
> >> know that template_list was read?
> >>
> >>> À: [log in to unmask]
> >>
> >>> Date: Mercredi 16 Septembre 2009, 17h15
> >>
> >>> Dear Gwenaelle,
> >>
> >>> Thank you again!
> >>
> >>>
> >>
> >>> I tried it out, however, and again i got 6
> timepoints
> >> in
> >>
> >>> the 4d template.
> >>
> >>>
> >>
> >>> I decided to copy my directory structure,
> maybe
> >> something
> >>
> >>> is wrong here, although i could not find
> what:
> >>
> >>>
> >>
> >>> vbmAga:
> >>
> >>> template list
> >> (containing:
> >>
> >>> 1101_struc.img
> >>
> >>> 1110_struc.img)
> >>
> >>> struc:
> >>
> >>> 1101_struc.hdr
> >>
> >>>
> >>
> >>> 1101_struc.img
> >>
> >>>
> >>
> >>> 1101_struc_GM.nii
> >>
> >>>
> >>
> >>>
> >> 1101_struc_GM_to_T.mat
> >>
> >>>
> >>
> >>>
> >> 1101_struc_GM_to_T.nii
> >>
> >>>
> >>
> >>> 1101_struc_GM_to_T_init.mat
> >>
> >>> 1101_struc_GM_to_T_init.nii
> >>
> >>> 1101_struc_GM_to_T_init_warp.msf
> >>
> >>> 1101_struc_GM_to_T_init_warp.nii
> >>
> >>>
> >> 1101_struc_GM_to_template_GM_init.log
> >>
> >>>
> >> 1101_struc_brain.hdr
> >>
> >>>
> >>
> >>>
> >> 1101_struc_brain.img
> >>
> >>>
> >>
> >>> 1101_struc_brain_mixeltype.nii
> >>
> >>>
> >>
> >>> 1101_struc_brain_pve_0.nii
> >>
> >>>
> >>
> >>> 1101_struc_brain_pve_2.nii
> >>
> >>>
> >>
> >>> 1101_struc_brain_pveseg.nii
> >>
> >>>
> >>
> >>> 1101_struc_brain_seg.nii
> >>
> >>>
> >>
> >>> 1110_struc.hdr
> >>
> >>>
> >>
> >>> 1110_struc.img
> >>
> >>>
> >>
> >>> 1110_struc_GM.nii
> >>
> >>>
> >>
> >>>
> >> 1110_struc_GM_to_T.mat
> >>
> >>>
> >>
> >>>
> >> 1110_struc_GM_to_T.nii
> >>
> >>>
> >>
> >>> 1110_struc_GM_to_T_init..mat
> >>
> >>>
> >>
> >>> 1110_struc_GM_to_T_init.nii
> >>
> >>>
> >>
> >>> 1110_struc_GM_to_T_init_warp.msf
> >>
> >>> 1110_struc_GM_to_T_init_warp.nii
> >>
> >>>
> >> 1110_struc_GM_to_template_GM_init.log
> >>
> >>>
> >> 1110_struc_brain.hdr
> >>
> >>>
> >>
> >>>
> >> 1110_struc_brain.img
> >>
> >>>
> >>
> >>> 1110_struc_brain_mixeltype.nii
> >>
> >>>
> >>
> >>> 1110_struc_brain_pve_0.nii
> >>
> >>>
> >>
> >>> 1110_struc_brain_pve_2.nii
> >>
> >>>
> >>
> >>> 1110_struc_brain_pveseg.nii
> >>
> >>>
> >>
> >>> 1110_struc_brain_seg.nii
> >>
> >>>
> >>
> >>> 1112_struc.hdr
> >>
> >>>
> >>
> >>> 1112_struc.img
> >>
> >>>
> >>
> >>> 1112_struc_GM.nii
> >>
> >>>
> >>
> >>>
> >> 1112_struc_GM_to_T.mat
> >>
> >>>
> >>
> >>>
> >> 1112_struc_GM_to_T.nii
> >>
> >>>
> >>
> >>> 1112_struc_GM_to_T_init.mat
> >>
> >>>
> >>
> >>> 1112_struc_GM_to_T_init.nii
> >>
> >>>
> >>
> >>> 1112_struc_GM_to_T_init_warp.msf
> >>
> >>> 1112_struc_GM_to_T_init_warp.nii
> >>
> >>>
> >> 1112_struc_GM_to_template_GM_init.log
> >>
> >>>
> >> 1112_struc_brain.hdr
> >>
> >>>
> >>
> >>>
> >> 1112_struc_brain.img
> >>
> >>>
> >>
> >>> 1112_struc_brain_mixeltype.nii
> >>
> >>>
> >>
> >>> 1112_struc_brain_pve_0.nii
> >>
> >>>
> >>
> >>> 1112_struc_brain_pve_2.nii
> >>
> >>>
> >>
> >>> 1112_struc_brain_pveseg..nii
> >>
> >>>
> >>
> >>> 1112_struc_brain_seg.nii
> >>
> >>>
> >>
> >>> fslvbm2a
> >>
> >>>
> >>
> >>> Is it possible that fslvbm doesnt "like" the
> >> ANALYZE
> >>
> >>> format?
> >>
> >>>
> >>
> >>> Thank you, best,
> >>
> >>> Aga
> >>
> >>>
> >>
> >>>
> >>
> >>>
> >>
> >>> -----Ursprüngliche Nachricht-----
> >>
> >>> Von: FSL - FMRIB's Software Library im
> Auftrag
> >> von
> >>
> >>> Gwenaëlle DOUAUD
> >>
> >>> Gesendet: Di 2009-09-15 16:09
> >>
> >>> An: FSL@JISCMAIL.AC..UK
> >>
> >>> Betreff: Re: [FSL] Re : [FSL] FSL-vbm: how do
> i know
> >> that
> >>
> >>> template_list was read?
> >>
> >>>
> >>
> >>> Hi Aga,
> >>
> >>>
> >>
> >>> you should have only 3 then 2 timepoints in
> your 4D
> >>
> >>> template with the newer versions of FSL-VBM.
> >>
> >>>
> >>
> >>>> 1101_struc.img
> >>
> >>>> 1101_struc.hdr
> >>
> >>>> 1110_struc.img
> >>
> >>>> 1110_struc.hdr
> >>
> >>>
> >>
> >>> This might be the problem.... Just try with:
> >>
> >>>
> >>
> >>> 1101_struc.img
> >>
> >>> 1110_struc.img
> >>
> >>>
> >>
> >>> in your template list and this should work
> fine.
> >>
> >>>
> >>
> >>> Cheers,
> >>
> >>> Gwenaelle
> >>
> >>>
> >>
> >>>
> >>
> >>>
> >>
> >>>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >
> >
>
|