Check the email archives for a recent message about epidewarp.fsl from 
Doug, there is a newer version that works with FSL 5.

On Tue, 17 Jun 2014, Elia S. wrote:

> 
> Hi Anastasia,
> The epidewarp.fsl gives me the following output:
> 
> FSLVersion 5.0.6
> FSLVerMaj 5
> FSL Version is 5.0.6, must be 3.X or 4.X
> 
> Either from script or command line.
> 
> Best,
> Elia.
> 
> 
> Date: Tue, 17 Jun 2014 09:17:58 -0400
> From: ayendiki@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
>
> 
> Hi Elia - This could very well be the case. Does the epidewarp.fsl command 
> give you any specific error message, or does it just not create an output?
> 
> a.y
> 
> On Tue, 17 Jun 2014, Elia S. wrote:
> 
> > Hi Anastasia,
> > Yes, launching the same command line from terminal produced the same error, but at the sa
> me
> > time we realized we were using the wrong magnetic/phase dicoms.....which weren't
> > magnetic/phase images at all.
> > Could that be the cause of the failure? I would answer the question myself but right now 
> I
> > don't have the correct images to test it.
> > 
> > Best,
> > Elia.
> > 
> > 
> > Date: Sun, 15 Jun 2014 07:21:28 -0400
> > From: ayendiki@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
> >
> > 
> > Hi Elia - It looks like this file didn't get created:
> > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
> > 
> > The command that was supposed to create it was epidewarp.fsl. You can find 
> > the command line that begins with "epidewarp.fsl" in the log file that you 
> > sent me. When you run that whole line directly from the unix command line, 
> > do you get any errors?
> > 
> > a.y
> > 
> > On Thu, 12 Jun 2014, Elia S. wrote:
> > 
> > > Dear Freesurfer community,
> > > Whenever i try to launch the tracula preprocessing, using  "set dob0 = 1 " and the foll
> ow
> > ing command
> > > line:
> > > 
> > > trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tr
> ac
> > ula.config
> > > 
> > > It stops, giving me errors like these:
> > > 
> > > niiRead(): error opening file
> > > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
> > > 
> > > ERROR: reading
> > > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii
> .g
> > z
> > > 
> > > While setting "dob0 = 0" everything runs smoothly.
> > > 
> > > Can you help me please?  I'll attach the log + dmrirc (tracula.config)
> > > 
> > > Best,
> > > Elia.
> > > 
> > > ---------------------------------------------------------------------------------------
> --
> > ----------
> > > -----------
> > > 
> > > Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> > > 
> > > Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS
> > > 
> > > Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20
> :4
> > 5 UTC 2013
> > > x86_64 x86_64 x86_64 GNU/Linux
> > > 
> > >
> > 
> > _______________________________________________ Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf
> er
> > The information in this e-mail is intended only for the person to whom it is addressed. I
> f
> > you believe this e-mail was sent to you in error and the e-mail contains patient
> > information, please contact the Partners Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you in error but does
> > not contain patient information, please contact the sender and properly dispose of the
> > e-mail.
> > 
> >
> 
> _______________________________________________ Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended only for the person to whom it is addressed. If
> you believe this e-mail was sent to you in error and the e-mail contains patient
> information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error but does
> not contain patient information, please contact the sender and properly dispose of the
> e-mail.
> 
>