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Thank you for the quick reply Gwenaelle. -rwxrwxrwx 1 root root 0 Nov 25 15:33 fslvbm2a.e17760.1 -rwxrwxrwx 1 root root 0 Nov 25 15:43 fslvbm2a.e17760.2 -rwxrwxrwx 1 root root 0 Nov 25 15:53 fslvbm2a.e17760.3 -rwxrwxrwx 1 root root 0 Nov 25 16:05 fslvbm2a.e17760.4 -rwxrwxrwx 1 root root 0 Nov 25 16:15 fslvbm2a.e17760.5 -rwxrwxrwx 1 root root 0 Nov 25 16:26 fslvbm2a.e17760.6 -rwxrwxrwx 1 root root 0 Nov 25 16:36 fslvbm2a.e17760.7 -rwxrwxrwx 1 root root 0 Nov 25 16:46 fslvbm2a.e17760.8 -rwxrwxrwx 1 root root 0 Nov 25 16:56 fslvbm2a.e17760.9 -rwxrwxrwx 1 root root 0 Nov 25 17:07 fslvbm2b.e19378.1 -rwxrwxrwx 1 root root 0 Nov 25 17:09 fslvbm2b.e19378.2 -rwxrwxrwx 1 root root 0 Nov 25 17:11 fslvbm2b.e19378.3 -rwxrwxrwx 1 root root 0 Nov 25 17:14 fslvbm2b.e19378.4 -rwxrwxrwx 1 root root 0 Nov 25 17:16 fslvbm2b.e19378.5 -rwxrwxrwx 1 root root 0 Nov 25 17:18 fslvbm2b.e19378.6 -rwxrwxrwx 1 root root 0 Nov 25 17:21 fslvbm2b.e19378.7 -rwxrwxrwx 1 root root 0 Nov 25 17:23 fslvbm2b.e19378.8 -rwxrwxrwx 1 root root 0 Nov 25 17:26 fslvbm2b.e19378.9 -rwxrwxrwx 1 root root 1732 Nov 25 17:29 fslvbm2c.e20279 -rwxrwxrwx 1 root root 4749 Nov 25 17:29 fslvbm2d.e20921.1 -rwxrwxrwx 1 root root 4749 Nov 25 17:29 fslvbm2d.e20921.2 -rwxrwxrwx 1 root root 4749 Nov 25 17:29 fslvbm2d.e20921.3 -rwxrwxrwx 1 root root 4749 Nov 25 17:30 fslvbm2d.e20921.4 -rwxrwxrwx 1 root root 4749 Nov 25 17:30 fslvbm2d.e20921.5 -rwxrwxrwx 1 root root 4749 Nov 25 17:30 fslvbm2d.e20921.6 -rwxrwxrwx 1 root root 4749 Nov 25 17:30 fslvbm2d.e20921.7 -rwxrwxrwx 1 root root 4749 Nov 25 17:30 fslvbm2d.e20921.8 -rwxrwxrwx 1 root root 4749 Nov 25 17:30 fslvbm2d.e20921.9 -rwxrwxrwx 1 root root 1752 Nov 25 17:30 fslvbm2e.e21868 Looks like I didn't notice fslvbm2c.e20279: ** ERROR (nifti_image_read): failed to find header file for 'n_001_T1.gz_struc_GM_to_T' ** ERROR: nifti_image_open(n_001_T1.gz_struc_GM_to_T): bad header info Error: failed to open file n_001_T1.gz_struc_GM_to_T Cannot open volume n_001_T1.gz_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 /usr/local/fsl/bin/fslswapdim: line 105: [: =: unary operator expected ** 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 /usr/local/fsl/bin/fslswapdim: line 113: [: -gt: unary operator expected ** 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 /usr/local/fsl/bin/fslswapdim: line 115: [: -gt: unary operator expected ** 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 Cannot open volume template_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 Cannot open volume template_GM for reading! ... or fslvbm2e.e21868: ** ERROR (nifti_image_read): failed to find header file for 'n_001_T1.gz_struc_GM_to_T_init' ** ERROR: nifti_image_open(n_001_T1.gz_struc_GM_to_T_init): bad header info Error: failed to open file n_001_T1.gz_struc_GM_to_T_init Cannot open volume n_001_T1.gz_struc_GM_to_T_init 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 /usr/local/fsl/bin/fslswapdim: line 105: [: =: unary operator expected ** 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 /usr/local/fsl/bin/fslswapdim: line 113: [: -gt: unary operator expected ** 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 /usr/local/fsl/bin/fslswapdim: line 115: [: -gt: unary operator expected ** 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 Cannot open volume template_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 Cannot open volume template_GM for reading! Michael On Thu, Nov 25, 2010 at 1:58 PM, Gwenaëlle DOUAUD <[log in to unmask]>wrote: > Hi Michael, > > presumably the script failed before the fslvbm2d stage. What is the result > of an ls -al fslvbm2?.e* ? > > Cheers, > Gwenaelle > > > > De: Michael B <[log in to unmask]> > > Objet: [FSL] fslvbm_2_template errors, but no template > > À: [log in to unmask] > > Date: Jeudi 25 novembre 2010, 18h00 > > Hi there, > > > > As a trial, I'm trying to run "fslvbm_2_template -n" on 9 > > subjects. Their T1 images were brain-extracted by a protocol > > besides that executed by "fsl_vbm_bet." From previous > > exchanges on the listserv, I've learned that I should do the > > following: > > - Create a "struc" directory, in which I should input the > > subjects' non-brain-extracted T1 images (*_struc.nii.gz) and > > brain-extracted T1 images (*_struc_brain.nii.gz). > > - I've also learned the importance of a correspondence > > between the contents of the template_list and those of the > > "struc" directory. > > > > The contents of the template_list: > > n_001_T1.nii.gz > > n_002_T1.nii.gz > > n_003_T1.nii.gz > > n_004_T1.nii.gz > > p_001_T1.nii.gz > > p_002_T1.nii.gz > > p_003_T1.nii.gz > > p_004_T1.nii.gz > > The contents of the "struc" directory: > > n_001_T1_struc.nii.gz > > n_002_T1_struc.nii.gz > > n_003_T1_struc.nii.gz > > n_004_T1_struc.nii.gz > > n_005_T1_struc.nii.gz > > n_001_T1_struc_brain.nii.gz > > n_002_T1_struc_brain.nii.gz > > n_003_T1_struc_brain.nii.gz > > n_004_T1_struc_brain.nii.gz > > n_005_T1_struc_brain.nii.gz > > p_001_T1_struc.nii.gz > > p_002_T1_struc.nii.gz > > p_003_T1_struc.nii.gz > > p_004_T1_struc.nii.gz > > p_001_T1_struc_brain.nii.gz > > p_002_T1_struc_brain.nii.gz > > p_003_T1_struc_brain.nii.gz > > p_004_T1_struc_brain.nii.gz > > > > "fslvbm_2_template -n" doesn't create template_GM_4D, but > > yields the following error message (fslvbm2d.e20921): > > -------------------------------------------------------------------- > > 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 > > -------------------------------------------------------------------- > > > >