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Hi Daniel, you need to put only the name of the structural images (e.g., num_19_20110923.nii.gz) in your template_list, not its entire path... If you change this (or use the template_list file I've attached instead), this should work. Cheers, Gwenaëlle -------------------------------------------------------------------- Gwenaëlle Douaud, PhD FMRIB Centre, University of Oxford John Radcliffe Hospital, Headington OX3 9DU Oxford UK Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717 www.fmrib.ox.ac.uk/~douaud -------------------------------------------------------------------- ________________________________ De : Daniel Cole <[log in to unmask]> À : [log in to unmask] Envoyé le : Mardi 20 novembre 2012 17h46 Objet : Re: [FSL] fslvbm_2_template - not reading struc_GM_to_T Here you are Gwenaëlle. Thanks for looking into this. Daniel On Tue, Nov 20, 2012 at 12:17 PM, Gwenaëlle DOUAUD <[log in to unmask]> wrote: Hi Daniel, > > >could you please give me exactly the output for an 'ls -al' in your vbm home directory, an 'ls -al struc/fslvbm2c*', 'ls -al struc/*_struc_GM_to_T.*' as well as a'more template_list'? > > >Cheers, >Gwenaëlle > >-------------------------------------------------------------------- >Gwenaëlle Douaud, PhD >FMRIB Centre, University of Oxford >John Radcliffe Hospital, Headington >OX3 9DU Oxford UK >Tel: +44 (0) 1865 222 523 >Fax: +44 (0) 1865 222 717 >www.fmrib.ox.ac.uk/~douaud >-------------------------------------------------------------------- > > >________________________________ > De : Daniel Cole <[log in to unmask]> >À : [log in to unmask] >Envoyé le : Mardi 20 novembre 2012 14h56 >Objet : [FSL] fslvbm_2_template - not reading struc_GM_to_T > > > >Hello FSLers, > > >I am rerunning template creation for VBM on Macaque monkeys. However my fslvbm_2_template contains an error in the "fslvbm2c.e70552" file. Here is the error message: > > >(directories removed) >"** ERROR (nifti_image_read): failed to find header file for '.../.../num_19_20110923_struc_GM_to_T' >** ERROR: nifti_image_open(.../.../num_19_20110923_struc_GM_to_T): bad header info >ERROR: failed to open file .../.../19_20_test/num_19_20110923_struc_GM_to_T >Cannot open volume .../.../19_20_test/num_19_20110923_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" > > >I find this error message particularly strange since the "num_19_20110923_struc_GM_to_T" .mat and .nii.gz files exist. This is the first file in my template_list (which I will upload) so for some reason the first call is failing and causing the others to fail as well. My template_list is the same as it was before when I had the template creation step working and is in my base fslvbm directory. > > >Any hints or suggestions would be much appreciated, >Daniel > > > >-- > >Daniel Cole >University of Rochester >Brain and Cognitive Sciences >[log in to unmask] > > > -- Daniel Cole University of Rochester Brain and Cognitive Sciences [log in to unmask]