It's hard to tell what's causing the error without seeing the entire trac-all.log. However, by glancing at your config file you seem to still have B0 inhomogeneity correction turned on (dob0 = 1) but without specifying any field map dicoms. I'd turn it off and see if that fixes it.
On Mon, 15 Dec 2014, Katherine Damme wrote:
Where would I be specifying a directory as an input/output?
I used the following cmd: /usr/local/freesurfer/bin/trac-all -prep -c dmri.fy
On Sun, Dec 14, 2014 at 7:12 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Katerine
the COR-* format is an old one that we don't use anymore. If you specify
a directory as an
input/output we will assume that it contains COR files, which is probably
what you are seeing.
cheers
Bruce
On Sun, 14 Dec 2014, Katherine Damme wrote:
At what point is the COR-*.info file made?
I got the following error:
corRead(): can't open file /media/Sokol/Subj/COR-.info
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/Sokol/Subj/...
Linux kate.ad.wcas.northwestern.edu 2.6.32-431.3.1.el6.x86_64 #1
SMP Fri Dec
13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Fri Dec 12 12:54:40 CST 2014
[ksd770@kate 041]# ls /media/Sokol/Subj/COR-*
On Thu, Dec 11, 2014 at 2:48 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
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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