There should be a few more lines at the top of the log file, showing the exact trac-all command line that was executed, etc. Is this the entire log file?
On Sat, 3 Jan 2015, Katherine Damme wrote:
Here is the log.
On Sat, Jan 3, 2015 at 9:19 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
It looks like it's not finding the file that you specify - not
like it's finding it but it's in the wrong format. But I can't
tell just from one line, I need to see the entire output of
trac-all, which is saved in trac-all.log.
On Fri, 2 Jan 2015, Katherine Damme wrote:
I still get the error:
mv -f
/home/k/ksd770/Desktop/Subj/042/dmri/dwi_orig_flip.mghdti.bvecs
/home/k/ksd770/Desktop/Subj/042/dmri/bvecs
mv: cannot stat
`/home/k/ksd770/Desktop/Subj/042/dmri/dwi_orig_flip.mghdti.bvecs':
No such
file or directory
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 Jan 2
18:55:26 CST 2015
Is there a way to avoid specifying a bvec/bval file
and allowing it to pull
this information from the dicom?
The bvec/bval files that I was specifying came from
previous processing of
the data with FSL-bedpost, could this be causing the
error?
On Wed, Dec 31, 2014 at 8:05 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
You need to follow the format of
$FREESURFER_HOME/bin/dmrirc.example. Enter
single files for
bvalfile and bvecfile, not lists of files.
On Wed, 31 Dec 2014, Katherine Damme wrote:
Now it is crashing giving me an if:
Expression
Syntax Error. See below
On Wed, Dec 31, 2014 at 7:27 PM,
Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Kate - It's not finding the
gradient table.
You'll have to
specify the gradient table and
b-value table
as you did for the
first subject.
You can use the same config file
for all your
subjects, see the
example in
$FREESURFER_HOME/bin/dmrirc.example.
Happy new year,
a.y
On Wed, 31 Dec 2014, Katherine
Damme wrote:
Hello Everyone!
I was able to get tracula to
run on one
subject but
I am now getting the
following error with my new
subjects.
mv: cannot stat
`/home/k/ksd770/Desktop/Subj/043/dmri/dwi_orig_flip.mghdti.bvecs':
No such
file or directory
Let me know if you have any
ideas why it
is not
makeing the
dwi_orig_flip.mghdti.bvecs
in the prep
Thank you and have a Happy
New Year!!!
On Thu, Dec 18, 2014 at 5:38
PM,
Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Kate - The option
to use
row-formatted
(instead of
column-formatted)
gradient tables
was added in
a tracula update
that came out after
freesurfer 5.3
was
released. If you want to
use this format, you
can download
the update
here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
You should make sure
to download
the same
build as your 5.3
build, which should be
the CentOS
6 64-bit,
based on this line
that I got from your
trac-all.log:
build-stamp.txt:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
a.y
On Wed, 17 Dec 2014,
Katherine
Damme wrote:
Thanks! That was
exactly it!
It was a
FAT server and
so that resolved
that issue.
Tracula is
claiming that the
bvecs and
bvals don't
have the same
number of
entries. These
were the
bvecs and bval
files created
during the
trac-all prep
process, but
when I
preprocesed the
data previously
with FSL the
bvecs and
bvals that
were created did
have equal
numbers. I
tried to specify
to use
these fsl made
bvecs and
bvals in the
configuration
file and it
continues to
default to the
ones that it
made.
Any ideas?
Thank you!
Kate
On Mon, Dec 15,
2014 at 7:42
PM, Watson,
Christopher
<christopher.wat...@childrens.harvard.edu> wrote:
I think
certain
filesystems don't
support sym
linking (e.g.
FAT32). So
that might be
it.
________________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]
on behalf
of Katherine
Damme
[katherine.da...@gmail.com]
Sent:
Monday, December
15, 2014
5:29 PM
To:
Anastasia Yendiki
Cc:
Freesurfer support
list
Subject:
Re:
[Freesurfer] From
bedpostX and
recon-all to
tracula
After
removing this I
have a new
(possibly
unrelated
error):
mv -f
/media/Sokol/Subj/041/dmri/bvecs
/media/Sokol/Subj/041/dmri/bvecs.norot
xfmrot
/media/Sokol/Subj/041/dmri/dwi.ecclog
/media/Sokol/Subj/041/dmri/bvecs.norot
/media/Sokol/Subj/041/dmri/bvecs
ln -sf
/media/Sokol/Subj/041/dmri/dwi.nii.gz
/media/Sokol/Subj/041/dmri/data.nii.gz
ln:
creating symbolic
link
`/media/Sokol/Subj/041/dmri/data.nii.gz': Operation
not permitted
This
persists even
when I run the
command as
the root user
and regardless
of the
permissions
settings of the
folder and
the
fdwi.nii.gz file.
Any ideas?
On Mon,
Dec 15, 2014
at 3:07 PM,
Anastasia
Yendiki
<ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>>
wrote:
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<mailto: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<http://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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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
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