Hi Eileen - In b0plist you can give files that contain either 2 phase maps (a volume with 2 frames), or the difference of 2 phase maps (a volume with only 1 frame). Depending on whether the volume that you specified has 2 or 1 frame, trac-all will assume which of the above you're giving it.

Your error seems to be that mri_convert doesn't recognize the format of your volume:

mri_convert /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII _T1_021210/dmri/b0pha.nii.gz niiRead(): unsupported datatype 32 (with scl_slope != 0) in /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii

Can you view the volume in freeview, for example? If freesurfer tools can't recognize the format of your file, then it's not a tracula-specific problem. In that case, it's best to send a new email on the list about the mri_convert error, so that you get responses from the appropriate experts.

a.y

On Wed, 27 Aug 2014, Eileen Moore wrote:

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.
  >       >
  >       >
  >       >
  >       >
  >
  >
  >
  >