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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: [log in to unmask] >> >>> 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 >> >>> >> >>> >> >>> >> >>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > >