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> Hi, > > Would it be possible to run Fugue using an already generated > phase difference map ? > > The field maps were acquired in two scans. There are two > magnitude images. The phase images already have a phase > difference calculated and has been unwrapped. The phase > difference is mapped onto the image range of 0 to 4095 > (original range -180 to +180 degrees). > > The following link seems to indicate that this might not be > possible > http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0310&L=fsl&P= I haven't tried this myself, so I'm not sure whether it will work, but it's worth a try if you don't get any other suggestions. If you have an unwrapped phase image, you can use that to create a pixel shift image using details of your EPI sequence and the field mapping sequence, using avwmaths. You can try to load the pixel shift map instead of the unwrapped phase image pair using the --loadshift option in fugue. I can't remember whether the pixel shift map intensity values are the shift in mm or voxels, so you could try scaling the image both ways. Dave