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 <ayend...@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.2.03.1407141119560.23...@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. > > > > > > > > > > > > _______________________________________________ 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.
