You get the same error as trac-all because trac-all runs mri_convert. I'd send the mri_convert error in a new email with mri_convert somewhere in the title, so that someone else can help you.
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Also when I run mir_convert on the DICOMs I get the same error as the one I
got when I used DICOMs :
WARNING:
file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.
45306.2014091812330393354083931 does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
Any idea what this could be ?
Thanks,
Ismail
On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail
<ikoub...@bwh.harvard.edu> wrote:
It says 1 … I don’t understand why I get that knowing that when I open
the nifti I can go through the frames …
Ismail
On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
I do not know why the dicoms do not work. When you run
mri_info on your nifti, what is the number of frames that
shows up?
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
This is what’s weird, my nifti volume contains
64 frames as my bvecs/bvals. So this shouldn’t
be the reason.
Also why the DICOMs wouldn’t work at the
beginning ?
Thanks,
Ismail
On Jul 4, 2016, at 2:41 PM,
Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>
wrote:
Hi Ismail - You can see from the
log file that the command that
causes the error is this:
mri_convert --frame 31
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
It's trying to extract the 32nd
frame of your nifti file, but from
the error message it looks like
your nifti file doesn't have a
32nd frame. So either the nifti
file has too few volumes, or the
bvecs/bvals have too many lines.
You'll have to figure that out.
a.y
On Mon, 4 Jul 2016, Koubiyr,
Ismail wrote:
Hi Anastasia,
Here it is.
But how could the
problem be related to
the nifti volume since
I have errors
when using the DICOMs
too ?
Thanks again,
Ismail
On Jul 4,
2016, at
1:44 PM,
Anastasia
Yendiki
<ayend...@nmr.mgh.harvard.edu>
wrote:
Hi Ismail
- It
sounds
like the
error has
to do with
the nifti
volume,
not
the bvecs/bvals. Can
you send the log file
from
scripts/trac-all.log?
Thanks,
a.y
On Mon, 4
Jul 2016,
Koubiyr,
Ismail
wrote:
Hi
Anastasia,
Thank
you
for
getting
back
to
me.
Here
are
more
details
about
my
problem,
I
think
it
should
help
you
understand
more.
I
run
trac-all
-prep
-c
on
some
DICOM
files
but
I
had
the
following
error
:
WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826
.0.1.368
0043
.6.8878.22551.20150806120704.648.1017
does
not
contain
a
Siemens
ASCII
header
has
this
file
been
anonymized?
ERROR:
cannot
unpack
mosiacs
without
ASCII
header
I
also
tried
to
de-mosiac
the
DICOMs,
it
gave
me
the
same
error.
Then
I
converted
the
DICOMs
into
NIFTI,
which
allowed
me
not
to
get
the
previous
error
but
something
else
weird
happened.
Now
I
get
:
ERROR:
fMRIframe:
frame
>=
nframes
I
checked
the
bvecs
and
bvals
files,
they
seem
normal,
no
additional
space,
but
when
the
new
bvecs
and
bvals
are
created,
they
seem
messed
up.
I
will
attach
you
all
the
bvecs
and
bvals
I
used
and
the
ones
I
get
too.
Ideally,
the
DICOMs
should
work
fine
but
I
have
no
idea
why
I
get
these
errors.
The
bvecs
and
bvals
are
obtained
from
dcm2nii
and
then
corrected
to
avoid
any
additional
space.
Thank
you
in
advance
for
your
help.
Best,
Ismail
P.S
:
3T2_bvecs.txt
and
3T2_bvals.txt
are
the
original
files
used.
On
Jul
4,
2016,
at
3:32
AM,
Anastasia
Yendiki
<ayend...@nmr.mgh.harvard.edu>
wrote:
Hi
Ismail
-
Are
you
passing
the
nifti
volume
as
input
to
trac-all?
It's
hard
to
tell
without
looking
at
your
configuration
file.
Best,
a.y
On
Tue,
28
Jun
2016,
Koubiyr,
Ismail
wrote:
Hi
everyone,
I
have
some
problems
trying
to
run
TRACULA
on
some
DWI
data.
It
is
a
mosaic
Siemens
DWI.
I
first
converted
the
DICOM
files
with
dcm2nii
to
get
the
bvec
and
bval
files.
Then
I
run
the
trac-all
-prep
-c
command
and
I
get
the
following
error
:
WARNING:
file
/My/path/to/dicom
does
not
contain
a
Siemens
ASCII
header
has
this
file
been
anonymized?
ERROR:
cannot
unpack
mosiacs
without
ASCII
header
I
tried
to
unpack
the
mosaics
with
gdcmtar,
but
I
got
the
same
error.
Thank
you
in
advance
for
your
help,
Ismail
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