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
>>
>>