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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