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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The information in this e-mail is intended only for the person
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contains patient information, please contact the Partners
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
