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Hi FSL experts I'm running FSL 5.0.11 on a cluster and cannot solve a problem with setup_masks I tried using setup_masks with FA data of a single MNI atlas tract (JHU.tract Forceps Major) to do a between group comparison. I masked the FA in each participant's individual space, then moved these masked FA tracts to MNI space. Since there is individual tract variability I created lesion-like FA masks, with 1's in the areas to be excluded for each participant, and 0's in the regions of their tract-FA. I then tried randomise_parallel on the cluster with the syntax suggested after running setup_mask (with either the -T or --T2 options) i.e., randomise -i all..dti.wls_FA.JHU.tract.9_Forceps_major.to.MNI152.merged.nii.gz -o all.dti.wls_FA.JHU.tract.9_Forceps_major.to.MNI152 -d all.setup_masks.FA.to.MNI.JHU.tract.9_Forceps_major.mat -t all.setup_masks.FA.to.MNI.JHU.tract.9_Forceps_major.con --vxl=-4 --vxf=all.setup_masks.FA.to.MNI.JHU.tract.9_Forceps_major -T (or --T2) -n 5000 Randomise runs, produces log files and the generate and defragement files as usual, but produces no tstat output files at all. Am I making an error in the randomise syntax? (the data seems fine, since I do get standard randomise output if I run randomise, with, for instance, the MNI atlas tract as the mask). Cheers James Hartzell Postdoctoral Fellow Basque Center on Cognition, Brain and Language Donostia, Spain 20003 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1