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Dear Dave, The command fslreorient2std does *not* align your image with standard space or transform it into standard space. It simply applies a 0, 90, 180 or 270 degree rotation to the image to get the axes in the best approximation to the standard space axes (e.g. turning "coronal" images into "axial"). To transform your mask into standard space you will need a transformation file (matrix or warp) from the space that the mask is originally in to the standard space and then use applywarp to transform it appropriately. To get the transformation file you will need to do a registration. If the mask was drawn on the subject's anatomical scan (highres) then it is highres2standard that you need (which may be a non-linear warp, in which case you must use applywarp). I hope this helps explain. If you are still unsure about this, look at the FSLCourse lecture and practical on image registration. All the best, Mark On 16 Nov 2011, at 14:35, David S Chester wrote: > Hi FSL Experts, > > I am running a group-level FEAT analysis with pre-threshold masking to an a priori ROI and I get this error every time in my Post-Stats log: > > /usr/local/fsl/bin/fslmaths thresh_zstat1 -mas /home/chester/Desktop/roi_masks/striatum/striatum_v1_oriented2std thresh_zstat1 > > WARNING:: Inconsistent orientations for individual images in pipeline! > Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*! > > Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > > echo 235753 > thresh_zstat1.vol > zstat1: DLH=0.0546938 VOLUME=235753 RESELS=86.1765 > > I am not sure what I'm doing wrong here. I used the fslorient2std command to correctly orient the mask images, and everything looks okay in FSLView. Please let me know if you have any ideas on what is going wrong here. > > Cheers, > Dave >