No, those are field maps used to correct for inhomogeneities in the main
magnetic field (which in MRI lingo is referred to as the B0 field, not to
be confused with the b=0 images). You can skip that correction (you have
to skip it if you don't have field maps).
On Thu, 11 Dec 2014, Katherine Damme wrote:
I am sorry, I am a bit confused. What am I supposed to be specifying under
the b0mlist and b0plist?
I thought that it was the B0 low-b image from diffusion.
Thank you!
On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Kate - The screenshot looks more like a low-b image from a
diffusion scan than a field map. In case this helps, the phase
map data will have either 2 volumes (2 phase maps acquired at
different echo times) or 1 volume (the difference of 2 such
phase maps).
Best,
a.y
On Thu, 11 Dec 2014, Katherine Damme wrote:
Hello
Has anyone else had the problem of tracula not
recognizing the format of the
phase map?
I opened the B0 in fslview and it appeared normal
(see screenshot). Any
help that you can offer would be greatly
appreciated! Thank you!
Thank you!
Kate Damme
On Fri, Nov 21, 2014 at 4:02 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Kate - The -prep, -bedp, and -path steps
need to be run
separately, in that order. You can't run them
all at once
unfortunately. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula
a.y
On Wed, 29 Oct 2014, Katherine Damme wrote:
Sorry for the delay. I signed up for the
course and
hoped that it would answer my question,
but I am
still
unsure what went wrong.
Thank you.
On Tue, Sep 9, 2014 at 12:14 PM,
Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Can you please attach the
trac-all.log file,
which has the entire output from
beginning to end?
Ofter something goes wrong earlier
that causes
the program to fail later in the
process.
Also, we'll need your original
configuration
file. Thanks!
On Mon, 8 Sep 2014, Katherine
Damme wrote:
Hello Freesurfer Community!
Thank you Anastasia and
Christopher, I
am still getting ending with errors and
the log
file gives no clue that I
have been able
to detect, see attached.
Any help would be
appreciated!
On Thu, Sep 4, 2014 at 4:29
PM,
Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>
wrote:
Hi Kate - There is an
example
configuration file for tracula in your
freesurfer
distribution
($FREESURFER_HOME/bin/dmrirc.example).
The same
file is also here:
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
If you attach your
configuration
file and the log file
(scripts/trac-all.log), we can try
to troubleshoot.
a.y
On Wed, 3 Sep 2014,
Katherine
Damme wrote:
> Hello Freesurfer
Community!
> I have sucessfully
completed
diffusion preprocessing in FSL and the
> recon-all of the
structural
image and would like to use tracula for
the
> tract
reconstruction. I keep
having trouble with my configuration
file.
>
> Does anyone have a
bedpostX
tracula config file they could share as
an
> example?H
>
> Thank you!
>
> Kate
>
>
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