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hi - I run flirt to derive individual space masks from a MNI one by using for i in 15AO 16KS 17RP 18AJ 19CL 20CJ 21CD 22EM 24MS 25NS 26TS 27LK 28AA 29DJ 30NS 31AK 32BS 33ES 34RR 36CG 37OF 38SI 39AH 40EE 41GW 42HM; do flirt -in /home/dsoto/Documents/fmri/uwm/rofc -ref /home/dsoto/Documents/fmri/uwm/$i/firstlevel.feat/example_func -applyxfm -init /home/dsoto/Documents/fmri/uwm/$i/firstlevel.feat/reg/standard2example_func.mat -out /home/dsoto/Documents/fmri/uwm/$i/indrofc; done it runs fine for most subjects, but for 7 of them it says terminate called after throwing an instance of 'NEWMAT::IncompatibleDimensionsException' Aborted I did not experience this issue before am using FSL 5.0.1 on Ubuntu 11.10 Cheers