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Subject:

: [FSL] FSL-vbm: template_list + template creation problems-continued

From:

"Burzynska, Aga" <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 23 Sep 2009 17:17:08 +0200

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (810 lines)

Hi,
I attached the tar file. I hope it works this way (is there other way to upload the files?).

Best,
Aga


-----UrsprŁngliche Nachricht-----
Von: FSL - FMRIB's Software Library im Auftrag von GwenaŽlle DOUAUD
Gesendet: Mi 2009-09-23 16:34
An: [log in to unmask]
Betreff: [FSL] Re : [FSL] AW: [FSL] Re : [FSL] FSL-vbm: template_list + template creation problems-continued
 
Hi again,

can you tar your vbm directory and upload it? I'll have a look at it...

Cheers,
Gwenaelle

--- En date de : Mer 23.9.09, Burzynska, Aga <[log in to unmask]> a ťcrit :

> De: Burzynska, Aga <[log in to unmask]>
> Objet: [FSL] AW: [FSL] Re : [FSL] FSL-vbm: template_list + template creation problems-continued
> ņ: [log in to unmask]
> Date: Mercredi 23 Septembre 2009, 14h57
> Hi Gwenaelle, 
> Here is ls of my vbm directory:
> struc       
>     template_list
> 
> and the contents of the template_list file we tried both:
> 1101_struc.img
> 1101_struc.hdr
> 1110_struc.img
> 1110_struc.hdr
> 
> 
> or:
> 1101_struc.img
> 1110_struc.img
> 
> Thank you for your help,
> best,
> Aga
> 
> 
> Betreff: [FSL] Re : [FSL] FSL-vbm: template_list + template
> creation problems-continued
>  
> Hi Aga,
> 
> could you give me the result of an ls in your fslvbm
> directory and copy the template_list file?
> 
> Cheers,
> Gwenaelle
> 
> --- En date de : Mer 23.9.09, Agnieszka Burzynska <[log in to unmask]>
> a ťcrit :
> 
> > De: Agnieszka Burzynska <[log in to unmask]>
> > Objet: [FSL] FSL-vbm: template_list + template
> creation problems-continued
> > ņ: [log in to unmask]
> > Date: Mercredi 23 Septembre 2009, 14h43
> > Dear Gwenaelle,
> > To solve this issue I decided to delete all recently
> > created files and run
> > fslvbm_2_template -n again. Below you find my outputs:
> the
> > template files
> > are missing.
> > 
> > 1101_struc.hdr       
>    
> >              
> > 1110_struc_brain_pve_0.nii
> > fslvbm2a.o98661.2 
> > 1101_struc.img       
>    
> >              
> > 1110_struc_brain_pve_2.nii
> > fslvbm2a.o98661.3 
> > 1101_struc_GM.nii       
>    
> >        
> >    1110_struc_brain_pveseg.nii
> > fslvbm2b 
> > 1101_struc_GM_to_T.mat     
>    
> >     
>    1110_struc_brain_seg.nii
> > fslvbm2b.e99177.1 
> > 1101_struc_GM_to_T.nii     
>    
> >         1112_struc.hdr
> > fslvbm2b.e99177.2 
> > 1101_struc_GM_to_T_init_warp.msf   
>    
> > 1112_struc.img
> > fslvbm2b.e99177.3 
> > 1101_struc_brain.hdr     
>    
> >       
>    1112_struc_GM.nii
> > fslvbm2b.o99177.1 
> > 1101_struc_brain.img     
>    
> >       
>    1112_struc_GM_to_T.mat
> > fslvbm2b.o99177.2 
> > 1101_struc_brain_mixeltype.nii   
>    
> >   1112_struc_GM_to_T.nii
> > fslvbm2b.o99177.3 
> > 1101_struc_brain_pve_0.nii   
>    
> >   
>    1112_struc_GM_to_T_init_warp.msf
> > fslvbm2c 
> > 1101_struc_brain_pve_2.nii   
>    
> >       1112_struc_brain.hdr
> > fslvbm2c.e99418 
> > 1101_struc_brain_pveseg.nii   
>    
> >      1112_struc_brain.img
> > fslvbm2c.o99418 
> > 1101_struc_brain_seg.nii     
>    
> >   
>    1112_struc_brain_mixeltype.nii
> > fslvbm2d 
> > 1110_struc.hdr       
>    
> >              
> > 1112_struc_brain_pve_0.nii
> > fslvbm2d.e99896.1 
> > 1110_struc.img       
>    
> >              
> > 1112_struc_brain_pve_2.nii
> > fslvbm2d.e99896.2 
> > 1110_struc_GM.nii       
>    
> >        
> >    1112_struc_brain_pveseg.nii
> > fslvbm2d.e99896.3 
> > 1110_struc_GM_to_T.mat     
>    
> >     
>    1112_struc_brain_seg.nii
> > fslvbm2d.o99896.1 
> > 1110_struc_GM_to_T.nii     
>    
> >         fslvbm2a
> > fslvbm2d.o99896.2 
> > 1110_struc_GM_to_T_init_warp.msf   
>    
> > fslvbm2a.e98661.1
> > fslvbm2d.o99896.3 
> > 1110_struc_brain.hdr     
>    
> >       
>    fslvbm2a.e98661.2
> > fslvbm2e 
> > 1110_struc_brain.img     
>    
> >       
>    fslvbm2a.e98661.3
> > fslvbm2e.e330 
> > 1110_struc_brain_mixeltype.nii   
>    
> >   fslvbm2a.o98661.1
> > fslvbm2e.o330 
> > 
> > The earlier error I traced appeared in 
> fslvbm2c.e
> > And contains:
> > 
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > '{
> > tf1nsinsicpg1252_struc_GM_to_T'
> > ** ERROR: nifti_image_open({
> > tf1nsinsicpg1252_struc_GM_to_T): bad header info
> > Error: failed to open file {
> > tf1nsinsicpg1252_struc_GM_to_T
> > Cannot open volume {
> > tf1nsinsicpg1252_struc_GM_to_T for reading!
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'template_4D_GM'
> > ** ERROR: nifti_image_open(template_4D_GM): bad
> header
> > info
> > Error: failed to open file template_4D_GM
> > Cannot open volume template_4D_GM for reading!
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'template_GM'
> > ** ERROR: nifti_image_open(template_GM): bad header
> info
> > Error: failed to open file template_GM
> > ERROR: Could not open file
> > /usr/local/fsl/bin/fslswapdim: line 105: [: =: unary
> > operator expected
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'template_GM'
> > ** ERROR: nifti_image_open(template_GM): bad header
> info
> > Error: failed to open file template_GM
> > ERROR: Could not open file
> > /usr/local/fsl/bin/fslswapdim: line 113: [: -gt:
> unary
> > operator expected
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'template_GM'
> > ** ERROR: nifti_image_open(template_GM): bad header
> info
> > Error: failed to open file template_GM
> > ERROR: Could not open file
> > /usr/local/fsl/bin/fslswapdim: line 115: [: -gt:
> unary
> > operator expected
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'template_GM'
> > ** ERROR: nifti_image_open(template_GM): bad header
> info
> > Error: failed to open file template_GM
> > Cannot open volume template_GM for reading!
> > ** ERROR (nifti_image_read): failed to find header
> file for
> > 'template_GM'
> > ** ERROR: nifti_image_open(template_GM): bad header
> info
> > Error: failed to open file template_GM
> > Cannot open volume template_GM for reading!
> > 
> > Thank you for your help!
> > 
> > Best,
> > Aga
> > 
> > 
> > 
> > 
> > On 9/17/09 6:00 PM, "GwenaŽlle DOUAUD" <[log in to unmask]>
> > wrote:
> > 
> > > 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 ťcrit :
> > > 
> > >> De: Agnieszka Burzynska <[log in to unmask]>
> > >> Objet: Re: [FSL] Re : [FSL] FSL-vbm: how do i
> know
> > that template_list was
> > >> read?
> > >> ņ: [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, "GwenaŽlle 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
> > >>> ťcrit :
> > >>> 
> > >>>> 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?
> > >>>> ņ: [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
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> -----UrsprŁngliche Nachricht-----
> > >>>> 
> > >>>> Von: FSL - FMRIB's Software Library
> im
> > Auftrag
> > >> von
> > >>>> GwenaŽlle 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 ťcrit :
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>>> De: Burzynska, Aga
> > >>>> <[log in to unmask]>
> > >>>> 
> > >>>>> Objet: [FSL] AW: [FSL] Re :
> [FSL]
> > FSL-vbm: how
> > >> do i
> > >>>> know that template_list was read?
> > >>>> 
> > >>>>> ņ: [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
> > >>>> 
> > >>>>> 
> > >>>> 
> > >>>>> 
> > >>>> 
> > >>>>> 
> > >>>> 
> > >>>>> -----UrsprŁngliche
> Nachricht-----
> > >>>> 
> > >>>>> Von: FSL - FMRIB's Software
> Library
> > im
> > >> Auftrag
> > >>>> von
> > >>>> 
> > >>>>> GwenaŽlle 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
> > >>>> 
> > >>>>> 
> > >>>> 
> > >>>>> 
> > >>>> 
> > >>>>>      
> > >>>> 
> > >>>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>>      
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>> 
> > >>>>  
> > >>>> 
> > >>> 
> > >>> 
> > >>> 
> > >> 
> > > 
> > > 
> > > 
> > 
> 
> 
>       
> 


      

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