Hi Gunjan our coordinate systems are extensively documented here:
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt cheers BruceOn Wed, 17 Dec 2014, Gunjan Gautam wrote:
Hi Bruce,
I can view the file using "freeview -v file.mnc" but I think that won't
solve my problem as I need to switch from 2D to 3D and vice versa.
I will be thankful if you could be a bit specific about "preserving the
direction cosine information" as I am facing difficulty to process these
volumes through FS.
Thanks,
Gunjan
On Tue, Dec 16, 2014 at 7:59 AM, Gunjan Gautam <gunjan.gemin...@gmail.com>
wrote:
Thank you Bruce,
I try this out.
On Dec 16, 2014 7:58 AM, "Bruce Fischl"
<fis...@nmr.mgh.harvard.edu> wrote:
I'm not sure what to tell you then. You need to save it in
a format that preserves the direction cosine information.
This shouldn't be that hard to do (e.g in matlab)
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
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