Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT)
From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] trac-all -prep error field map error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1407141119560.23459@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"


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.
>
>
>
>