Bruce
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
I think that won't resolve my issue because I need to deal with a specific
set of noise removal algorithms and nonuniformity correction algorithms.
On Dec 16, 2014 7:50 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
have you tried just giving the original volume to recon-all? We
typically deal with this kind of thing internally (and in 3D,
not on a slice-by-slice basis)
cheers
Bruce
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
Sure,
My data(3D volume) is having different ranges of
noise and nonuniformity so
I want to apply different algorithms to get rid of
these and analyze the
extent.
On Dec 16, 2014 7:40 AM, "Bruce Fischl"
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Gunjan
can you elaborate? What kind of modifications
would you want to
make to each slice?
Bruce
On Tue, 16 Dec 2014, Gunjan Gautam wrote:
Yes Bruce, minc is a volume but I want
to perform
some experiments and see
the aftereffects.
This is how I come from 3D to 2D to make
changes in
each slice and again I
rejoin these slices (2D to 3D). I don't
know if
anything other than NIfTi
gives this much flexibility or it could
be dealt
without coming in 2D space.
Any suggestion will be highly
appreciate.
On Dec 16, 2014 7:22 AM, "Bruce Fischl"
<fis...@nmr.mgh.harvard.edu> wrote:
isn't the minc a volume? It
certainly supports
holding an entire
volume in a single file
On Tue, 16 Dec 2014, Gunjan Gautam
wrote:
Ok , I try this out.
I converted it to nii
because after
processing 2D
slices of the volume, I
can easily switch to 3D
space(ie
stacking) in order
to apply brain
extraction tools as NIfTi
provides some
of the
useful utilities.
On Dec 16, 2014 6:59 AM,
"Bruce Fischl"
<fis...@nmr.mgh.harvard.edu>
wrote:
why do you need to
convert it to
nifti? Can
you process the minc
directly? See if
freeview can
display it:
freeview -v file.mnc
On Tue, 16 Dec 2014,
Gunjan Gautam
wrote:
Hi Bruce,
Originally, data
was in MINC
format.
On Dec 16, 2014
1:54 AM,
"Bruce Fischl"
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Gunjan
what was
the original
data format
that you
had? Once you
have
converted
it to nifti
in your
current stream
you can no
longer
use the
data, so you
have to start
further
upstream
cheers
Bruce
On Tue, 16
Dec 2014,
Gunjan Gautam
wrote:
I
don't have
dicom for this
subject but
it can
easily be
converted to from
.nii
to .dcm.
I
try this out
and get back
to you if I
stuck at
some
point.
Thanks,
Gunjan
On
Dec 16, 2014
12:49 AM,
"Bruce Fischl"
<fis...@nmr.mgh.harvard.edu>
wrote:
do you
have the dicom
data for
this subject?
If
so, it will
be
separated
into
different "series"
each
corresponding to
one
acquisition (e.g. a
T1-weighted
one such as
mprage or
FLASH).
Typically
that series
will have
more than 150
slices (since
that's
what it takes
to cover the
brain at
close to 1mm
voxel
size). You
need to
give recon-all
the dicom
file
that
contains a
single one
of those
slices. It
doesn't matter
which one - we
will
figure out the
rest of them
from any of
them
On Tue, 16
Dec 2014,
Gunjan Gautam
wrote:
Hi
Bruce,
I am
sorry to
say that I did
not get you
properly.
Could you please
say a bit
more about "a
*single*
slice in the
correct
series ". I want
to try this
option.
On
Dec 16, 2014
12:13 AM,
"Bruce Fischl"
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Gunjan
freesurfer
will handle
the dicom
slices just
find. Just give
recon-all
a *single*
slice in the
correct
series with the
-i
command
and it should
work. I
don't know
medcon, but it
is not
propagating the
direction cosine
info
into the
nifti, which
means that
the nifti
files are
effectively
useless as you
will
never be
able to
distinguish left
from
right
again
cheers
Bruce
On Tue, 16
Dec 2014,
Gunjan Gautam
wrote:
Thanks Bruce,
I
used "medcon"
command
(Ubuntu) for the
stacking of
2D
slices in
order to
convert it in a
volume.
These slices
were
obtained
from
a volume
itself and
after making
some intensity
changes, a
volume is
formed (using
medcon)
again. Then I
fed this
volume as input
to
FS in
order to extract
brain.
Can
I overcome
this
orientation
issue ?
Gunjan
On
Dec 15, 2014
11:49 PM,
"Bruce Fischl"
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Gunjan
the
problem is that
the
nifti
volume doesn't
contain the
direction
cosine
information that
we
need to
figure out what
directions
are A/P,
I/S
and L/R.
mri_convert
warns of this:
mri_convert
m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-00001.nii.gz
test.mgz
mri_convert
m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-00001.nii.gz
test.mgz
$Id:
mri_convert.c,v
1.213
2014/07/29
19:22:31
fischl Exp $
reading
from
m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-00001.nii.gz...
WARNING:
neither
NIfTI-1 qform or
sform are
valid
WARNING:
your volume
will
probably
be
incorrectly
oriented
TR=1.00,
TE=0.00,
TI=0.00, flip
angle=0.00
WARNING:
it does not
appear that
there was
sufficient
information
in the
input to assign
orientation
to
the
volume...
i_ras =
(-1, 0, 0)
j_ras =
(0, 1, 0)
k_ras =
(0, 0, 1)
writing to
test.mgz...
and if you
try to view
the
converted volume
in
freeview it
shows
up in the
wrong
orientation (e.g
what
we think
is
"coronal" is
actually
horizonatal).
How did
you create the
nifti
files? If you
give
dicom
directly
to
recon-all you
will
likely not
have
this
problem
cheers
Bruce
On Thu, 11
Dec 2014,
Gunjan Gautam
wrote:
Dear
all,
I am
facing few
errors in
recon-all
command (eg
mritotal failed)
while
dealing with a
specific set
of
volumes.
How
to
overcome these
issues in
order to run
recon-all
successfully.
Please find the
recon-all.log
and volume
attached
with
this mail.
Gunjan
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