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Dear FSL experts, I have a couple of questions to ask about 1- I think this one is a bug: if you try to do integer pixel shifts using flirt (like this) > flirt -in spgr.hdr -ref spgr.hdr -out upspgr.hdr -init up1.mat - > applyxfm where up1.mat contains an INTEGER z-direction shift only, flirt doesn't do anything at all to the image. With non-integer shifts it works fine though. 2. I think that this other one is lack of knowing the correct usage: Lets say that I run mcflrt on a time series of images (structs.img) and produce rstructs.mat/MAT000* series of matrices. I want to apply those MAT transformations to a set of corresponding field maps. applyxfm4D fmaps.img r_fmaps.img fmaps.img rstructs.mat -fourdigit The resulting rotated images have crazy rotations/translations (except fot the first one) even though the original realigned structurals have been realigned properly. Could someone tell me what's wrong? What are the units in the .par files? is it mm and degrees? Thank you very much, -Luis Begin forwarded message: > From: "Robert Welsh" <[log in to unmask]> > Date: July 13, 2005 2:47:37 PM EDT > To: <[log in to unmask]> > Subject: flirt command > > > bug is when the transformation matrix appears to have unit voxel > shift. > > flirt -in spgr.hdr -ref spgr.hdr -out upspgr.hdr -init up1.mat - > applyxfm > > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > Robert C. Welsh, PhD > Research Investigator > Department of Radiology > University of Michigan > (734) - 764 - 2412 (fax) > [log in to unmask] > > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and > should not be used for urgent or sensitive issues. > >