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
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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