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Hello, I'm trying to look at hippocampal volumes from a range of subjects. (1) If I run_first_all without specifying an output file name, I get different output files to if I run_first_all with an output file specified. Can anyone explain why? I presume specifying an output filename is the best way to proceed? (Details of which files listed below). (2) If I run fslstats -V on some of these output files, I get quite different results. Of the three measures that seem to make reasonable sense, can anyone advise on the most realistic measure of hippocampal volume? fslstats NAME-L_Hipp_first.nii.gz -V (obtained from both output and non-output run_first_all) 3478 4576.762695 fslstats NAME-L_Hipp_corr.nii.gz -V (obtained from output run_first_all only) 2665 3506.921387 fslstats -L_Hipp_corr_grot.nii.gz -V (obtained from non-output run_first_all only) 1642 2160.737305 Thanks very much in advance, Duncan SPECIFIED OUTPUT (-o): run_first_all -i IMAGENAME -b -s L_Hipp -o NAME image_spgr_axial.img_to_std_sub.mat GIVES: NAME.com NAME-L_Hipp_first.nii.gz IMAGENAME_spgr_axial_to_std_sub.nii.gz NAME-L_Hipp_corr.nii.gz NAME-L_Hipp_first.vtk NAME-L_Hipp_first.bvars NAME.logs IMAGENAME_spgr_axial_to_std_sub.mat NON-SPECIFIED OUTPUT: run_first_all -i IMAGENAME -b -s L_Hipp image_spgr_axial.img_to_std_sub.mat GIVES: NAME.logs -L_Hipp_corr_t1_roi.nii.gz -L_Hipp_first.nii.gz -L_Hipp_corr_grot.nii.gz -L_Hipp_corr_trans_roi.mat -L_Hipp_first.vtk IMAGENAME_spgr_axial_to_std_sub.mat -L_Hipp_corr_lb_roi.nii.gz -L_Hipp_first.bvars IMAGENAME_spgr_axial_to_std_sub.nii.gz