Hi Steve
Thank you very much for your help. I think the problem was in my
template_list file. It is now running ok.
Cheers
Reem
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf Of Stephen Smith
Sent: Wednesday, October 06, 2010 8:53 PM
To: [log in to unmask]
Subject: Re: [FSL] fslvbm_2_template not creating a template_GM_4D
Hi - you can see that the first (i.e. earliest) error file (*.e*) is
fslvbm2c.e343 - what does it say in that file?
This is where GM segmentations get averaged to create a study-specific
template - maybe you are using an incorrect template_list file?
Cheers.
On 4 Oct 2010, at 03:32, Reem Jan wrote:
> Dear Steve
>
> Thank you for looking into this for me. Please find attached an MS
word file (ReemVBM.docx) with the output of "ls -lart". I tried to send
you a .txt file but my email got rejected due to being too large, so I
have had to paste the output into Microsoft Word, I hope this is ok.
>
> I ran this command inside the 'struc' directory which contains no
subdirectories apart from 'slicesdir'.
>
> Many thanks
> Reem
>
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf Of Stephen Smith
> Sent: Saturday, October 02, 2010 6:58 PM
> To: [log in to unmask]
> Subject: Re: [FSL] fslvbm_2_template not creating a template_GM_4D
>
> Hi - I suggest that you send us the result of running "ls -lart" in
the output directory and any subdirectories......that will help work out
how far things got.
> Cheers.
>
>
> On 30 Sep 2010, at 05:21, Reem Jan wrote:
>
>
> Dear FSLers
>
> This is my first try at VBM analysis, I have run into a problem and I
would really appreciate some advice.
>
> I ran the command line: fslvbm_2_template -n and the job was done,
however the template_GM_4D and the GM mirror images were not created?
>
> From looking at old archives, I found some recommendations to look at
the fslvbm2.o and .e files. I observed the following:
>
> There were "fslvbm2a.o and .e" & "fslvbm2b.o and .e" & "fslvbm2d.o and
.e" files for every subject. However, there weren't "fslvbm2c.o and .e"
nor "fslvbm2e.o and .e" files for each subject.
>
> Also, when I tried opening these files in a text editor, they were
empty and contained no text.
>
> I'm not sure what this means or why the template_GM_4D and the GM
mirror images were not created.
>
> Any ideas? J
>
> Cheers
> Reem
>
>
>
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------------------------------------------------------------------------
---
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
------------------------------------------------------------------------
---
>
>
>
>
>
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signature database 5500 (20101003) __________
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> http://www.eset.com
> <ReemVBM.docx>
------------------------------------------------------------------------
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
---
__________ Information from ESET NOD32 Antivirus, version of virus
signature database 5510 (20101006) __________
The message was checked by ESET NOD32 Antivirus.
http://www.eset.com
__________ Information from ESET NOD32 Antivirus, version of virus
signature database 5510 (20101006) __________
The message was checked by ESET NOD32 Antivirus.
http://www.eset.com
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