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
>>
>>>
>>
>>>
>>
>>>
>>
>>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
>
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