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.
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
-
Anastasia Yendiki -
Eileen Moore