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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