On Jun 14, 2016, at 8:52 AM, Marja Caverlé <marja.caverle@gmail.com> wrote:Hi Bruce,
I did not get any error message, the page just remained empty after selecting the files. Maybe my files were the reason why it didn't work.
Best,
Marja_______________________________________________On Tue, Jun 14, 2016 at 10:50 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:freeview works fine with most dicoms. Do you get an error message?
On Tue, 14 Jun 2016, Marja Caverlé wrote:
Hi Bruce,
When I wanted to view them in freeview, simply nothing happened. Freeview
did not load the files, so I assumed it did not work with dicoms, that's why
I converted them.
Best,
Marja
On Tue, Jun 14, 2016 at 12:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu>
wrote:
What do you mean that FS did not accept the dicom files? Can you
provide a command line and terminal output? You can use
dcmunpack -src /path/to/dicom to get a list of the series in a
dicom folder
On 6/13/16 9:57 PM, Marja Caverlé wrote:
Hi Bruce,
I converted first of all because freesurfer did not accept
the dicom files. Furthermore the dicom's consist of a lot
of files of different scans, and they are not named
accordingly. The whole folder consists of files called eg
1254890234, so I have no clue how to get the right files.
Thanks!
On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
Hi Marja
why are you converting at all? Why not just give one
of the dicom files in the correct series to
recon-all directly? I don't think we've ever seen an
orientation problem if you process that way
cheers
Bruce
On Tue, 14 Jun 2016, Marja Caverlé wrote:
No, when I view them in freeview the
orientation is the same as in the
original dicoms, but the results in the
.stats files made me think that left
and right might be swapped. Of course
this could just really be the results
of the correct hemispheres, but that is
why I asked whether you are aware of
any dimension switching during the
recon-all. If not, than I can safely
assume that the results are correct.
Best,
Marja
On Tue, Jun 14, 2016 at 1:29 AM, Bruce
Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
so you convert from dicom to
nifti, then view in freeview and
you think that the anatomical
orientations are incorrect? That
should definitely not be the case
On Tue, 14 Jun 2016, Marja Caverlé
wrote:
Well the DICOMs I visualized
in osiriX, and the
niftis in both freesurfer
and fsl. And there they
seemed to match.
So my question is; is there
a possibility that
dimensions are swapped
during
the recon -all? If not, then
I am sure R=R and L=L.
Thanks!
On Tue, Jun 14, 2016 at
12:55 AM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi Marja
what did you visualize
it in? I would suggest
freeview
cheers
Bruce
On Tue, 14 Jun 2016,
Marja Caverlé wrote:
Hi Bruce,
I converted the
images with MRIconvert,
then I
swapped them in
FSL with
swapdim.
I checked the
images by opening the
original dicoms
and the
converted
niftis, and then
visually compared them
(since the
heads are not
very
symmetrical that
was not too hard).
Best,
Marja
On Tue, Jun 14,
2016 at 12:35 AM, Bruce
Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi Marja
how did
you swap them? And more
importantly,
how did you
check
that the
orientations were correct
after
conversion?
cheers
Bruce
On Mon, 13
Jun 2016, Marja Caverlé
wrote:
Hi
guys,
Just
a quick question; I
have converted
my original
DICOMs into niftis.
After the conversion I
manually checked
whether the
orientations were still
the
same, and they were not,
so I
swapped them.
After this I did a recon
-all.
A
lot of my results are at
one side
while I expected
them
in the other
hemisphere. Is there any
chance that the
recon -all
swapped left and right?
How
to check for this? I
just want to be
sure that I
am
really talking about
the
right hemisphere.
Thanks!
Best,
Marja
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