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Hi, These scripts are in $FSLDIR/bin If you open a terminal and type: echo $FSLDIR/bin then it will print this location (which can be different on different machines). You will need to use the cost function weighting options with your masks for the registration calls within these scripts in order to take into account your lesion masks. All the best, Mark On 24 Nov 2014, at 10:28, Rosalia Dacosta Aguayo <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear FSL expersts, I am trying to edit fslvbm_2_template or fsl_reg following instructions found in the fsl mailing list: The problem is that I do not know where are those scripts in order to modify them.... I masked the lesions, binarized and thresholded them with fslmaths and give them a value of 0 (fslmaths mul)....but I still do not know how to mask them out of the brains....and how to find the fslvbm_2_script in order to make the changes..... Any suggestion would be very appreciate, Yours sincerely, Rosalia. > I'm trying to run fsl-vbm on lesioned brains. As expected, > after running fslvbm_2_template, I noticed that the grey > matter images (subject_struc_GM's) include not only grey > matter, but also lesions. I, therefore, masked out the > lesions, creating masked grey matter images > (subject_struc_GM_masked's). I would now like to rerun > fslvbm_2_template and the remainder of the fsl-vbm protocol > using these images. I guess there are two ways of dealing with lesions: either you use the masks when using fnirt (in which case you need to edit the call to fsl_reg in the fslvbm scripts), or you mask out the lesions in the GM images (what you've done). If the latter, you then simply need to call the masked GM images _struc_GM (save the original GM images with lesions somewhere else or under a different name) and then run an edited fslvbm_2_template locally in your vbm directory, by just removing the lines 96 to 104 (simple # in front of it will do) and deleting "-j $fslvbm2a_id" from line 112.