Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example?

As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium).

In the tutorial dmrirc example I see only the 'set b0mlist' and 'set b0plist' options, and am unsure where I could give it the phase difference map.

I've also tried converting the dicom magnitude and phase maps to nifti format and inputting these into the dmrirc file but I am still getting an error. (See attached log file).

Thanks,
Eileen.



------------------------------

Message: 10
Date: Thu, 17 Jul 2014 04:14:16 -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.2.03.1407170411110.12767@nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed


Hi Eileen - All image formats that mri_convert (and thus any freesurfer
program) can read will do, you don't need dicom. Try giving trac-all the
phase difference maps you have and let's see what happens.

Best,
a.y

On Wed, 16 Jul 2014, Eileen Moore wrote:

> Hi Anastasia,
>
> OK - our imaging physicists had developed a wrapper script around epidewarp
> which takes our dicom images and converts them into the phase difference map
> (it is based on the script that was authored by Doug Greve for the fBIRN
> consortium). It looks like the tracula script requires dicom images. Is
> there a way for me to do epidewarp manually and then follow through with the
> remaining steps using trac-all?
>
> Thanks,
> Eileen.
>
>
>       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.
>       >
>       >
>       >
>       >
>
>
>
>