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 <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.2.03.1407170411110.12...@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 <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.
> >
> >
> >
> >
>
>
>
>
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