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Hi Matthew, Thank you for replying. Here is the command-line, and respective messages: neuroimaging@neuroimgaing-Dell2:/ws_mprage_FSL$ fslvbm_2_template -a CON_wsMRI_007-0002-00001-000176-01_struc CON_wsMRI_009-0002-00001-000176-01_struc CON_wsMRI_023-0002-00001-000176-01_struc CON_wsMRI_024-0002-00001-000176-01_struc CON_wsMRI_025-0002-00001-000176-01_struc CON_wsMRI_031-0002-00001-000176-01_struc CON_wsMRI_032-0002-00001-000176-01_struc PAT_wsMRI_011-0002-00001-000176-01_struc PAT_wsMRI_013-0002-00001-000176-01_struc PAT_wsMRI_014-0002-00001-000176-01_struc PAT_wsMRI_017-0002-00001-000176-01_struc PAT_wsMRI_019-0002-00001-000176-01_struc PAT_wsMRI_027-0002-00001-000176-01_struc PAT_wsMRI_030-0004-00001-000176-01_struc Running segmentation: ID=64873 Running initial registration: ID=65671 /usr/share/fsl/5.0/bin/fsl_sub: 410: exit: Illegal number: -1 Creating first-pass template: ID=The command you have requested cannot be found or is not executable /usr/share/fsl/5.0/bin/fsl_sub: 410: exit: Illegal number: -1 Running registration to first-pass template: ID=The command you have requested cannot be found or is not executable /usr/share/fsl/5.0/bin/fsl_sub: 410: exit: Illegal number: -1 Creating second-pass template: ID=The command you have requested cannot be found or is not executable Study-specific template will be created, when complete, check results with: fslview struc/template_4D_GM and turn on the movie loop to check all subjects, then run: fslview /usr/share/fsl/5.0/data/standard/tissuepriors/avg152T1_gray struc/template_GM to check general alignment of mean GM template vs. original standard space template. neuroimaging@neuroimgaing-Dell2:/ws_mprage_FSL$ The *.e* files in ./struc all have zero-size. I checked this by running the command-line: neuroimaging@neuroimgaing-Dell2:/ws_mprage_FSL$ ls -l ./struc/*.e* -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:42 ./struc/fslvbm2a.e64873.1 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:46 ./struc/fslvbm2a.e64873.10 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:46 ./struc/fslvbm2a.e64873.11 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:47 ./struc/fslvbm2a.e64873.12 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:47 ./struc/fslvbm2a.e64873.13 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:47 ./struc/fslvbm2a.e64873.14 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:42 ./struc/fslvbm2a.e64873.2 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:43 ./struc/fslvbm2a.e64873.3 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:43 ./struc/fslvbm2a.e64873.4 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:44 ./struc/fslvbm2a.e64873.5 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:44 ./struc/fslvbm2a.e64873.6 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:44 ./struc/fslvbm2a.e64873.7 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:45 ./struc/fslvbm2a.e64873.8 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:45 ./struc/fslvbm2a.e64873.9 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:48 ./struc/fslvbm2b.e65671.1 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:50 ./struc/fslvbm2b.e65671.10 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:50 ./struc/fslvbm2b.e65671.11 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:50 ./struc/fslvbm2b.e65671.12 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:50 ./struc/fslvbm2b.e65671.13 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:51 ./struc/fslvbm2b.e65671.14 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:48 ./struc/fslvbm2b.e65671.2 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:48 ./struc/fslvbm2b.e65671.3 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:49 ./struc/fslvbm2b.e65671.4 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:49 ./struc/fslvbm2b.e65671.5 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:49 ./struc/fslvbm2b.e65671.6 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:49 ./struc/fslvbm2b.e65671.7 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:49 ./struc/fslvbm2b.e65671.8 -rw------- 1 neuroimaging neuroimaging 0 Sep 14 09:50 ./struc/fslvbm2b.e65671.9 neuroimaging@neuroimgaing-Dell2:/ws_mprage_FSL$ Do you know what I need to do? Cheers, Nicolas Nicolás Francisco Lori, PhD University of Minho ICVS | School of Medicine Campus Gualtar 4710-057 Braga Portugal Professional email: [log in to unmask] ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1