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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 > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature database 5490 (20100929) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > --------------------------------------------------------------------------- > 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 5500 (20101003) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > __________ Information from ESET NOD32 Antivirus, version of virus signature database 5500 (20101003) __________ > > The message was checked by ESET NOD32 Antivirus. > > 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 ---------------------------------------------------------------------------