Hi,
the problem is coming from what you've entered in your template_list: you entered (first line) the name of this image that does not exist. Subsequently, the first-pass template is not created, then the second one...
Try rerunning fslvbm_2 with the correct names in the template_list, it should be fine...
Cheers,
Gwenaelle
PS: The two versions I mentioned were of the template_list, not of fslvbm_2.
--- En date de : Mar 9.9.08, Antonios - Constantine Thanellas <[log in to unmask]> a écrit :
> De: Antonios - Constantine Thanellas <[log in to unmask]>
> Objet: Re: [FSL] following different order on VBM analysis steps+in addition
> À: [log in to unmask]
> Date: Mardi 9 Septembre 2008, 14h28
> Hello again Gwenaelle,
>
> I've modifed the fslvbm_2_template as you've
> proposed and the run was more
> normal this time.Though the template_GM_4D image was not
> created.I've
> noticed the following errors:
> 1st) Even though my template list contains 36 (out of the
> 38 files,since
> according to the guides the same amount of controls and
> patients should be
> used) ,it seems that the script processes all the files
> (i've seen that the
> same issue has been reported in the fsl list with the
> title: "VBM template
> creation with selected images")
>
> 2nd) an error fslvbm2e.e10389 report which is very strange
> for the following
> reason: It mentions that:
> ** ERROR (nifti_image_read): failed to find header file for
> '01_CON_002_S_0295_SC_struc_GM_to_T_init'
> ** ERROR:
> nifti_image_open(01_CON_002_S_0295_SC_struc_GM_to_T_init):
> bad
> header info
>
> and the strange thing is that 01_CON_002_S_0295_SC file
> does not exist.This
> file actually is the 20_CON_002_S_0295_SC.
>
> In order for this to be more clarified find attached the
> .txt files that
> were created during the analysis + the structure of my
> folder were the
> analysis took place.
> Thank you
>
>
> On Mon, 8 Sep 2008 14:30:24 +0100, Antonios - Constantine
> Thanellas
> <[log in to unmask]> wrote:
>
> >Yes Gwenaelle,
> >I work with an AMD athlon 64 ,3200+, with 1GB RAM and a
> SATA hard disk. My
> >platform is Ubuntu 7.10 (gutsy) and i use the FSL 4.1.0
> version. All my data
> > (brain images) come though from a previous version of
> fsl (FSL 4.0) and
> >ubuntu (7.04).
> >As i've already mentioned i bypassed the first step
> of VBM analysis since i
> >had already my brain images extracted and i confronted
> this problem when i
> >was trying to run the script fslvbm_2_template -n.
> >Find attached an fslerroreport that may give you some
> more info regarding my
> >system and my environmental variables.
> >In case you need some more information ,just inform me
> >Thank you
> >
> >
> >On Mon, 8 Sep 2008 12:30:56 +0000, Gwenaëlle DOUAUD
> ><[log in to unmask]> wrote:
> >
> >>Hi Antonios - Constantine,
> >>
> >>this is exactly the problem, you're right. I
> know about this script (since
> >I've written it with Steve), this is why I asked
> you the output of imglob as
> >it was the only problem I could think of :-).
> >>
> >>It would be interesting for us to know why
> you've got such problem. So
> >could you please give me as much details as possible:
> e.g., on which machine
> >are you working, with which kind of environment etc.?
> >>
> >>To solve your problem for the moment, try replacing
> `$FSLDIR/bin/imglob
> >*_struc.*` by `$FSLDIR/bin/remove_ext *_struc.*`
> throughout the
> >fslvbm_2_template and fslvbm_3_proc scripts. It should
> work fine...
> >>
> >>Cheers,
> >>Gwenaelle
> >>
> >>
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