Hi Eileen - That step is run with the program epidewarp.fsl, which you can run on the command line to see the available options. The input phase map volume is expected to have either 2 frames (2 separate phase maps) or 1 frame (the difference phase map). This error from trac-all means that it found that your input phase map has something other than 1 or 2 frames, so it doesn't know how to handle it.
Hope this helps, a.y On Sat, 12 Jul 2014, Eileen Moore wrote:
Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: "ERROR: Unrecognized format of phase map". However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks, Eileen.
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