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
<fis...@nmr.mgh.harvard.edu <mailto:fis...@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
<fis...@nmr.mgh.harvard.edu <mailto:fis...@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
<fis...@nmr.mgh.harvard.edu
<mailto:fis...@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
<fis...@nmr.mgh.harvard.edu
<mailto:fis...@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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