Hi - I still have not been able to apply the field map correction within tracula. Tracula does not appear to recognize the format of my field maps in either dicom or nifti formats. However, as a work around I first did the field map correction outside tracula (using our wrapper script for epidewarp). Next I used this field map corrected image as the input diffusion image for tracula and set dob0 = 0 in my dmrirc file (so as to skip tracula's field map correction). This appears to be working.
Eileen.
Message: 5 Date: Wed, 27 Aug 2014 13:51:06 -0700 From: Eileen Moore eimoore@mail.sdsu.edu Subject: Re: [Freesurfer] trac-all -prep error field map error To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: <CA++dajQo_2EF= LvUFCKbs+_061v7dcTFC5T11PN0K4G9d-CuAw@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
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. > > > >
freesurfer@nmr.mgh.harvard.edu
-
Eileen Moore