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Dear Gwenaëlle, Thank you very much for your response. To my surprise many of the original images from these 2 subjects are ok. e.g. the images from the subj which does not appear in the template are as follows: _struc_ _GM_ _struc_GM_to_T _struc_GM_to_T_init _struc_GM_to_T_init_warp..., are ok when checking in fslview. However, the: _struc_GM_to_template_GM _struc_GM_to_template_GM_mod _struc_GM_to_template_GM_warp _struc_JAC_nl..., when oppened in fslview are NaNs. Do you have some clue what could have happened? I will try anyway with fslroi/fslmerge to discard them, but it would be great if i can solve it in order not to make the sample too short. Thanks again! Juan Blas Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Gwenaëlle DOUAUD Gesendet: Dienstag, 10. April 2012 18:01 An: [log in to unmask] Betreff: [FSL] Re : [FSL] template_GM_4D Hi Juan Blas, not sure what's happening here, but quite likely flirt or fnirt (affine/NL registration) has failed for these two subjects. You need to have a look at the original _struc and _GM images to understand why. If there is no way of recovering these images, then you can just use fslroi/fslmerge on template_GM_4D to edit these two out. Then average with fslmaths, flip the result with fslswapdim, and average the two to obtain a symmetric template. 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<http://www.fmrib.ox.ac.uk/~douaud> -------------------------------------------------------------------- ________________________________ De : "Couto, Blas" <[log in to unmask]> À : [log in to unmask] Envoyé le : Mardi 10 avril 2012 13h08 Objet : [FSL] template_GM_4D Dear FSLers, I´am quite new at FSL and have been trying the fslvbm script with a sample of 20 patients and 21 controls. After the fslvbm_2_template step had finished, I took a look at the file template_GM_4D with fslview motion loop tool, and realized there are two no proper slices (number 7th: NaN, and number 37th: weird zoomed image). I would like to know how to edit this template in order to continue with step 3 of fslvbm, and if does any of you have any idea on why this errors occur? Thanks in advance, Cheers, Juan Blas