Thanks.

Using:

mri_convert dicom output.nii -iid 0 -1 0 -ijd 0 0 -1 -ikd -1 0 0

Seems to do the trick.

I have attached a figure with the left image from mri_convert and the right image using mri_convert and the flags listed above, both viewed using tkmedit.

From a visual perspective I prefer the right hand image, and wonder if this striping appearance in the left hand image is smoothed when creating orig.mgz using the --conform flag?

Would using:

mri_convert dicom output.nii -iid 0 -1 0 -ijd 0 0 -1 -ikd -1 0 0

mri_convert output.nii orig.mgz --conform

be preferred (or acceptable) in this case?

Paul

I don't think this is aproblem either. tkmedit/freeview will be showing
it in the acquisition RAS space (not the image coordinate space). I
don't think there is anything wrong with the actual data. If the volumes
from other packages do not show up this way in tkmedit/fv then it may
mean that they are throwing away this information. You can throw it away
too when you run mri_convert, something like

mri_convert dicom output.nii -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1

see if that at least causes the funny images to go away.


On 04/27/2014 10:35 PM, prasser wrote:
> Thanks for your reply.
>
> Yes, I can upload the data. Is there a private area I can upload to?
>
> Also, is there a flag that enables acquisition slice space info to be
> used with tkmedit?
>
> Lastly, when converting to .nii with other packages and viewing with
> tkmedit the acquisition slice space seems to be taken into account.
>
> Paul
>
>
>
>
>
> ---- On Sun, 27 Apr 2014 17:33:02 -0700 *Bruce Fischl
> <fischl@nmr.mgh.harvard.edu>* wrote ----
>
> Hi Paul
>
> perhaps Ruopeng can comment, but I suspect this isn't a problem -
> it's
> just showing it to you in a standard anatomical space not the
> slice spaceit
> was acquired in. If you want to upload the dataset we can take a
> look and
> confirm
>
> cheers
> Bruce
>
>
> On Sun, 27 Apr 2014, prasser wrote:
>
> > Hi,
> >
> > I am still having some concerns using mri_convert on Skyra
> volumes that I'm
> > hoping can please be addressed.
> >
> > On this occasion I have used mri_convert to convert a single
> dicom file to
> > nifti from a volume collected on a siemens Skyra scanner using
> Freesurfer5.3
> > on CentOS5.7.
> >
> > When viewing this nifti image using tkmedit it appears 'cut-up'
> over many
> > sagittal slices (please see attached) rather than the whole
> image appearing
> > on one plane.
> >
> > Not sure if this is an issue with tkmedit or mri_convert?
> >
> > This problem persists if i convert the entire volume, with this
> 'cutting'
> > appearing as vertical lines in the image.
> >
> > This is also the case when using the new mri_convert patch for
> OS X.
> >
> > Lastly, I can upload a dicom file if needed.
> >
> > Thanks,
> > Paul
> >
> >
> >
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