Hi Gunjancan 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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